Comprehensive Microbial Resource

www.tigr.org/CMR

Bioinformatics Visualization Bioinformatics Visualization WorkshopWorkshop

Owen WhiteOwen White

May 30, 2002May 30, 2002

Curation Genome AnnotationGenome Annotation

Michelle GwinnMichelle Gwinn Bob DodsonBob Dodson Bob DeBoyBob DeBoy James KolonayJames Kolonay Bill NelsonBill Nelson Ramana MadupuRamana Madupu Sean DaughertySean Daugherty Maureen BeananMaureen Beanan Scott DurkinScott Durkin Lauren BrinkacLauren Brinkac

Bioinformatics EngineersBioinformatics Engineers Jeremy PetersonJeremy Peterson Lowell UmayamLowell Umayam Samual AngiuoliSamual Angiuoli

TIGRFAMs/GroupsTIGRFAMs/Groups Dan HaftDan Haft Jeremy SelengutJeremy Selengut

Maria Ermolaeva Maria Ermolaeva (Operons/Terminators)(Operons/Terminators)

Erik Ferlanti (All vs. All)Erik Ferlanti (All vs. All) FacultyFaculty

Jonathan Eisen (DNA Jonathan Eisen (DNA repair)repair)

Ian Paulsen Ian Paulsen (transporters)(transporters)

Steven Salzberg Steven Salzberg CollaboratorsCollaborators

Swiss-protSwiss-prot Monica RileyMonica Riley The open source crowdThe open source crowd Art Delcher (Glimmer)Art Delcher (Glimmer)

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-Caudal Fins

http://web.pdx.edu/~bowersn/bi399/lecture2.html

Caudal FinsDorsal Spines Dorsal Rays

Retrieval across data types.

Typical annotation datatypesclone_info: Tracks information related to the parent nucleotide assembly, including its annotation status,

which institution the sequence was derived, and whether it is part of a larger assembly such as a chromosome.

asm_feature: All major features of the parent assembly are stored here, including annotated genes, predicted genes, repetitive elements, splice sites, and all underlying components of a gene (models, transcript exons, and cds exons).

phys_ev: Attribute for each gene component within the asm_feature table. For example, each predicted and annotated gene has a model and multiple exons stored in the asm_feature table. Linking the feature to phys_ev will identify the type of feature present: ie. glimmer, genscan+, genemarkHMM, or working (annotation). This becomes important if a single feature in the asm_feature table is shared by multiple model types.

feat_link: This table is key to the principles behind representing gene models in the database. All parent and child relationships are defined here.

evidence: The main repository for all sequence database search results. Also, it retains information regarding gene model attributes such as the best blast match and all Pfam matches.

ident: Stores attributes for the highest element of the gene component hierarchy, the transcriptional unit. Gene names, loci, EC symbols, and other attributes are available.

role_link: The role category assignments for each gene are available here. Roles include examples such as ‘transcription’, ‘DNA synthesis’, ‘translation’, ‘DNA repair’, ‘amino acid metabolism’, etc.

Omniome Content, GenesTotal # of genes: 132,998 from world-wide effort. (43,311 TIGR projects). 36,274 w/ genetic names. 15,098 genes placed into 5,451 paralogous

families.

413 rRNAs.

1311 tRNAs.

49 sRNAs.

293 IS elements.

Omniome ContentEvidence: 1073 distinct EC#s, assigned to 17308 genes Rows of allVall data:  3,996,851 Rows of HMM TIGRFAM data: 91,550 Rows of HMM Pfam data: 131,963 Rows of COG data: 149,940 Rows of Interpro data: 175,760 Rows of Prosite data: 53,132 Rows of BER data: 91,899

TIGRFAM Matrix

The Genome Browser: Linear Display of DNA Molecules

Genome vs. Genome Protein Hits

MUMmer: The Whole Genome Alignment Tool

Role Category Graph

Multi-Genome Query ToolQuery across all genomes based on different properties MW, pI, membrane spanning regions Taxon, Paralogous families, TIGRFAMs, Role

Category Best Match to: organism, locus, kingdom, etc.

“Genes with >5 membrane spanning regions and MW 36,000-51,000d.”

“E. coli genes with best match to Archeoglobis involved in DNA metabolism.”

Pseudo-Restriction Digest and Linear Depiction of Cuts

Position effect: