![Page 1: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/1.jpg)
March 28 2002
NIH Proteomics Workshop
Bethesda MD
Lai-Su Yeh PhD
Protein Scientist National Biomedical Research Foundation
Demo Demo Protein Information ResourceProtein Information Resource
2
Database DemoDatabase DemoNREF Database httppirgeorgetownedupirwwwsearchpirnrefshtml
iProClass Database httppirgeorgetowneduiproclasshtml iProClass Sequence (A58910) Motif (PCM00487)
PIR-PSD Database httppirgeorgetowneducgi-binpirwwwnbrfgetampuid=A58910 PIR Entry (A58910)
Other Molecular Databases Function KEGG Enzyme (EC 111205) KEGG Pathway (
MAP00230) BRENDA (EC 111205) Structure PDB (1AK5) SCOP (1003001006002002) CATH
(1AK5) Family Pfam (PF00478) BLOCKS (BL00487) PROSITE
(PS00487)
3
PIR Web Site PIR Web Site (httppirgeorgetownedu)(httppirgeorgetownedu)
4
Text Search Result with Text Search Result with NULLNOT NULLNULLNOT NULL
5
Peptide Search ResultsPeptide Search Results
6
PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 2: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/2.jpg)
2
Database DemoDatabase DemoNREF Database httppirgeorgetownedupirwwwsearchpirnrefshtml
iProClass Database httppirgeorgetowneduiproclasshtml iProClass Sequence (A58910) Motif (PCM00487)
PIR-PSD Database httppirgeorgetowneducgi-binpirwwwnbrfgetampuid=A58910 PIR Entry (A58910)
Other Molecular Databases Function KEGG Enzyme (EC 111205) KEGG Pathway (
MAP00230) BRENDA (EC 111205) Structure PDB (1AK5) SCOP (1003001006002002) CATH
(1AK5) Family Pfam (PF00478) BLOCKS (BL00487) PROSITE
(PS00487)
3
PIR Web Site PIR Web Site (httppirgeorgetownedu)(httppirgeorgetownedu)
4
Text Search Result with Text Search Result with NULLNOT NULLNULLNOT NULL
5
Peptide Search ResultsPeptide Search Results
6
PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 3: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/3.jpg)
3
PIR Web Site PIR Web Site (httppirgeorgetownedu)(httppirgeorgetownedu)
4
Text Search Result with Text Search Result with NULLNOT NULLNULLNOT NULL
5
Peptide Search ResultsPeptide Search Results
6
PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 4: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/4.jpg)
4
Text Search Result with Text Search Result with NULLNOT NULLNULLNOT NULL
5
Peptide Search ResultsPeptide Search Results
6
PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 5: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/5.jpg)
5
Peptide Search ResultsPeptide Search Results
6
PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 6: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/6.jpg)
6
PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 7: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/7.jpg)
7
PIR-NREF Search Result (II)PIR-NREF Search Result (II)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 8: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/8.jpg)
9
PIR Pattern SearchPIR Pattern Search
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 9: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/9.jpg)
10
PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml
Pattern Match Sequence vs PROSITE
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 10: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/10.jpg)
11
PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 11: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/11.jpg)
12
PIR Domain Display PIR Domain Display
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 12: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/12.jpg)
13
PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)
search
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 13: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/13.jpg)
14
PIR-NREF ReportPIR-NREF Report
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 14: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/14.jpg)
15
PIR-iProClass DatabasePIR-iProClass Database
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 15: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/15.jpg)
16
iProClass Sequence ReportiProClass Sequence Report
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 16: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/16.jpg)
17
PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 17: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/17.jpg)
18
Related Sequences Related Sequences
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 18: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/18.jpg)
19
Protein Family ClassificationProtein Family Classification
Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture
Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research
Discovery of New Knowledge by Using Information Embedded within
Families of Homologous Sequences and Their Structures
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 19: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/19.jpg)
20
Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions
Family A Set of Protein Sequences That Share a Common
Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)
Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)
Overall Sequence Identity gt=45
Superfamily A Set of Protein Families That Share a Common Evolutionary
Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 20: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/20.jpg)
21
Protein Domain DefinitionProtein Domain Definition
Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)
A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 21: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/21.jpg)
22
Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 22: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/22.jpg)
23
iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001
Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 23: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/23.jpg)
24
iProClass Superfamily ReportiProClass Superfamily Report
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 24: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/24.jpg)
25
Alignment and Tree ViewAlignment and Tree View
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 25: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/25.jpg)
26
PIR-Protein Sequence DatabasePIR-Protein Sequence Database
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 26: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/26.jpg)
27
PIR-PSD EntryPIR-PSD Entry
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 27: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/27.jpg)
28
BLASTFASTA SearchBLASTFASTA Search
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 28: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/28.jpg)
29
PIR FASTA Search ResultPIR FASTA Search Result
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 29: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/29.jpg)
30
PIR Searches and AligmentPIR Searches and Aligment BLAST Search
Multiple Alignment amp Tree View
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 30: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/30.jpg)
31
PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml
HMM Model Building amp Sequence Search
One Protein Against All HMMs
All Proteins Against One HMM
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 31: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/31.jpg)
33
Bibliography SubmissionBibliography Submission
View Bibliography Information
View Protein Entry
Submit Citation with Optional Categorization
S1
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 32: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/32.jpg)
34
Bibliography Information Display (I)Bibliography Information Display (I)
From PIR-NREF
From Other Curated Database (eg SGD)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 33: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/33.jpg)
35
Bibliography Information Display (II)Bibliography Information Display (II)
From User Submission
From Computer-Mapping (eg Gene Symbol)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 34: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/34.jpg)
36
Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)
WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-
![Page 35: March 28, 2002 NIH Proteomics Workshop Bethesda, MD Lai-Su Yeh, Ph.D. Protein Scientist, National Biomedical Research Foundation Demo: Protein Information](https://reader035.vdocument.in/reader035/viewer/2022062805/5697c0221a28abf838cd3972/html5/thumbnails/35.jpg)
37
Proteomic BioinformaticsProteomic Bioinformatics
Large-Scale Analysis of Proteomic Data Homology Search for Pathways
- Database Demo
- PIR Web Site (httppirgeorgetownedu)
- Text Search Result with NULLNOT NULL
- Peptide Search Results
- PIR-NREF Search Result (I)
- PIR-NREF Search Result (II)
- PIR Pattern Search
- PIR Pattern Search Result (I)
- PIR Pattern Search Result (II)
- PIR Domain Display
- PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
- PIR-NREF Report
- PIR-iProClass Database
- iProClass Sequence Report
- PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
- Related Sequences
- Protein Family Classification
- Protein FamilySuperfamily Definitions
- Protein Domain Definition
- Superfamily-Domain-Motif Relationship
- iProClass Superfamily List
- iProClass Superfamily Report
- Alignment and Tree View
- PIR-Protein Sequence Database
- PIR-PSD Entry
- BLASTFASTA Search
- PIR FASTA Search Result
- PIR Searches and Aligment
- PIR Hidden Markov Model
- Bibliography Submission
- Bibliography Information Display (I)
- Bibliography Information Display (II)
- Oracle Demo
- Proteomic Bioinformatics
-