interpro/prosite ucsc genome browser exercise 3. turning information into knowledge the outcome of...
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InterPro/prosite InterPro/prosite UCSC Genome UCSC Genome
BrowserBrowser
Exercise 3Exercise 3
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Turning information into knowledgeTurning information into knowledge
The outcome of a sequencing project is The outcome of a sequencing project is masses of raw datamasses of raw data
The challenge is to turn this The challenge is to turn this raw data into raw data into biological knowledgebiological knowledge
A valuable tool for this challenge is an A valuable tool for this challenge is an automated diagnostic pipe through which automated diagnostic pipe through which newly determined sequences can be newly determined sequences can be streamlinedstreamlined
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From sequence to functionFrom sequence to function
Nature tends to innovate rather than inventNature tends to innovate rather than invent Proteins are composed of functional Proteins are composed of functional
elements: domains and motifselements: domains and motifs DomainsDomains are structural units that carry out a are structural units that carry out a
certain functioncertain function The same domains are The same domains are
shared between different shared between different proteinsproteins
MotifsMotifs are shorter are shorter sequences with certainsequences with certainbiological activitybiological activity
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http://www.ebi.ac.uk/http://www.ebi.ac.uk/interprointerpro//
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InterProInterPro
An integrated documentation resource for An integrated documentation resource for protein families, domains and sitesprotein families, domains and sites
Groups signatures describing the same protein Groups signatures describing the same protein family or domainfamily or domain
Combines a number of databases that use Combines a number of databases that use different methodologies to derive protein different methodologies to derive protein signature:signature: UniProt: UniProtKB Swiss-Prot, TrEMBL, UniProt: UniProtKB Swiss-Prot, TrEMBL,
UniRef,UniParcUniRef,UniParc prosite: documented DB on domains, families and prosite: documented DB on domains, families and
functional sites.functional sites. Pfam: a DB of protein families represented by MSAsPfam: a DB of protein families represented by MSAs
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Member databasesMember databases
SequenceSequence--motif methods:motif methods: Protein signature DBs with different Protein signature DBs with different
focusfocus
SequenceSequence--cluster methods:cluster methods: Hierarchically clustered Hierarchically clustered
sequence/structure DBssequence/structure DBs
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InterPro searchInterPro search
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http://www.expasy.ch/http://www.expasy.ch/prositeprosite//
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prositeprosite
A method for determining the function of A method for determining the function of uncharacterized translated protein uncharacterized translated protein sequencessequences
Consists of a DB of annotated biologically Consists of a DB of annotated biologically important important sites/patterns/motifs/signature/fingerprintssites/patterns/motifs/signature/fingerprints
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prositeprosite Entries are represented with Entries are represented with patternspatterns or or
profilesprofiles
pattern
1122334455
AA0.660.66110000..
TT00000011..
CC0.330.33000.660.6600..
GG00000.330.3300..
profile
[AC-]A-[GC]-T-[TC]-[GC]
Profiles are used in prosite when the motif is relatively Profiles are used in prosite when the motif is relatively divergent, and it is difficult to represent as a patterndivergent, and it is difficult to represent as a pattern
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Scanning prositeScanning prosite
Query: sequence
Query: pattern
Result: all patterns found in sequence
Result: all sequences which adhere to this pattern
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Patterns with a high probability of Patterns with a high probability of occurrenceoccurrence
Entries describing commonly found postEntries describing commonly found post--translational modifications or compositionally translational modifications or compositionally biased regions.biased regions.
Found in the majority of known protein Found in the majority of known protein sequences sequences
High probability of occurrenceHigh probability of occurrence
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prosite sequence queryprosite sequence query
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prosite pattern queryprosite pattern query
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UCSC Genome BrowserUCSC Genome Browser
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Reset all settings of
previous user
UCSC Genome Browser - GatewayUCSC Genome Browser - Gateway
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UCSC Genome Browser - GatewayUCSC Genome Browser - Gateway
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UCSC Genome Browser - GatewayUCSC Genome Browser - Gateway
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UCSC Genome BrowserUCSC Genome Browserquery resultsquery results
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UCSC Genome Browser UCSC Genome Browser Annotation tracksAnnotation tracks
Vertebrate conservation
mRNA (GenBank)
RefSeq
UCSC Genes
Base position
Single species compared
SNPs
Repeats
GeneDirection
Exon
Intron
UTR
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USCS GeneUSCS Gene
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UCSC Genome Browser - movementUCSC Genome Browser - movement
Zoom x3 + Center
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UCSC Genome Browser – UCSC Genome Browser – Base viewBase view
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Annotation track optionsAnnotation track options
dense
squish
full
pack
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Annotation track optionsAnnotation track optionsAnother option totoggle between
‘pack’ and ‘dense’view is to click on
the track title
Sickle-cell anemia distr.
Malariadistr.
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BLATBLAT
BLAT = BBLAT = Blast-last-LLike ike AAlignment lignment TTool ool BLAT is designed to find similarity of BLAT is designed to find similarity of >95% on >95% on
DNADNA, , >80% for protein>80% for protein Rapid search by indexing entire genome.Rapid search by indexing entire genome.
Good for:Good for:
1.1. Finding genomic coordinates of cDNAFinding genomic coordinates of cDNA
2.2. Determining exons/intronsDetermining exons/introns
3.3. Finding human (or chimp, dog, cow…) Finding human (or chimp, dog, cow…) homologs of another vertebrate sequencehomologs of another vertebrate sequence
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BLAT on UCSC Genome BrowserBLAT on UCSC Genome Browser
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BLAT on UCSC Genome BrowserBLAT on UCSC Genome Browser
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BLAT ResultsBLAT Results
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BLAT ResultsBLAT Results
Match
Non-Match(mismatch/indel)
Indel boundaries
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BLAT ResultsBLAT Results
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BLAT Results on the browserBLAT Results on the browser
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Getting Getting DNADNA sequence of region sequence of region
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Getting Getting DNADNA sequence of region sequence of region