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Comprehensive Microbial Resource www.tigr.org/CMR

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Caudal Fins. http://web.pdx.edu/~bowersn/bi399/lecture2.html. Caudal Fins. Dorsal Spines ... which institution the sequence was derived, and whether it is part ... – PowerPoint PPT presentation

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Title: Comprehensive Microbial Resource www.tigr.org/CMR


1
Comprehensive Microbial Resourcewww.tigr.org/CMR
Bioinformatics Visualization Workshop Owen
White May 30, 2002
2
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)

3
Retrieval
Caudal Fins
Heterocercal- Forked- Lunate- Emarginate- Truncate
- Rounded- Pointed-
http//web.pdx.edu/bowersn/bi399/lecture2.html
4
Retrieval across data types.
Caudal Fins
Dorsal Spines
Dorsal Rays
5
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.

6
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.

7
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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11
TIGRFAM Matrix
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14
The Genome Browser Linear Display of DNA
Molecules
15
Genome vs. Genome Protein Hits
16
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.

25
Pseudo-Restriction Digest and Linear Depiction of
Cuts
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28
Position effect
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