Comprehensive Microbial Resource www.tigr.org/CMR

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Comprehensive Microbial Resourcewww.tigr.org/CMR
Bioinformatics Visualization Workshop Owen
White May 30, 2002
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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)

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Retrieval
Caudal Fins
Heterocercal- Forked- Lunate- Emarginate- Truncate
- Rounded- Pointed-
http//web.pdx.edu/bowersn/bi399/lecture2.html
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Retrieval across data types.
Caudal Fins
Dorsal Spines
Dorsal Rays
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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.

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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.
• 1311 tRNAs.
• 49 sRNAs.
• 293 IS elements.

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Omniome Content

• Evidence
• 1073 distinct ECs, 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

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TIGRFAM Matrix
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The Genome Browser Linear Display of DNA
Molecules
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Genome vs. Genome Protein Hits
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MUMmer The Whole Genome Alignment Tool
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Role Category Graph
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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 gt5 membrane spanning regions and MW
  36,000-51,000d.
• E. coli genes with best match to Archeoglobis
  involved in DNA metabolism.

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Pseudo-Restriction Digest and Linear Depiction of
Cuts
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Position effect