Comprehensive Microbial Resource Bioinformatics Visualization Workshop Owen White May 30, 2002

Curation  Genome Annotation  Michelle Gwinn  Bob Dodson  Bob DeBoy  James Kolonay  Bill Nelson  Ramana Madupu  Sean Daugherty  Maureen Beanan  Scott Durkin  Lauren Brinkac  Bioinformatics Engineers  Jeremy Peterson  Lowell Umayam  Samual Angiuoli  TIGRFAMs/Groups  Dan Haft  Jeremy Selengut  Maria Ermolaeva (Operons/Terminators)  Erik Ferlanti (All vs. All)  Faculty  Jonathan Eisen (DNA repair)  Ian Paulsen (transporters)  Steven Salzberg  Collaborators  Swiss-prot  Monica Riley  The open source crowd  Art Delcher (Glimmer)

Retrieval Heterocercal- Forked- Lunate- Emarginate- Truncate- Rounded- Pointed- Caudal Fins

Caudal FinsDorsal SpinesDorsal Rays Retrieval across data types.

Typical annotation datatypes clone_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, Genes Total # 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 tRNAs. 49 sRNAs. 293 IS elements.

Omniome Content Evidence: 1073 distinct EC#s, assigned to 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 Tool Query 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: