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OrthoMCL DB

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013d-8e3b-8e69-2ed7-105480000000

Resource Type

  1. Database

Properties

  1. Related Software
    OrthoMCL
  2. Resource Description
    Ortholog Groups of Protein Sequences from 150 genomes which contain 1398546 protein sequences. "For each ortholog group, we provide basic information and other useful data about the group: a). Size of the group, in terms of both number of sequences and number of taxa. b). Sequence similarity info, indicating the degree of conservation within the group: % Match Pairs (percentage of all possible pairs within the group that are matched through BLAST under the default cutoff, and the rest of similarity info is calculated based on these matched pairs only), Average E-value, Average % Coverage, and Average % Identity. c). Phyletic profile, displaying #sequences from each species that belong to this ortholog group; black box indicates presence (with the number below the genome abbreviation representing #sequences) while white box stands for absence. d). Keywords: the most frequently occurring keywords in the annotations of the member sequences. e). Pfam domains: the most frequently occurring Pfam domains in the member sequences. f). Pfam domain architecture: useful to compare among group members and to identify outliers (due to evolution or sequencing/gene model errors). e). BioLayout graph, displaying the sequence similarity relationship between group members together with OrthoMCL edge information (in the SVG version of the graph). f). Multiple Sequence Alignment of the ortholog group."
  3. Used by
    Computational Biology and Informatics Laboratory
  4. Version
    5
  5. Data Input
    Genomes
  6. Related Publication or Documentation
    OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
  7. Related Publication or Documentation
    OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
  8. Related Publication or Documentation
    Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes
  9. Website(s)
    http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi
  10. Developed by
    Stoeckert, Christian J., Jr., Ph.D.
  11. Developed by
    Chen, Feng, Ph.D.
  12. Developed by
    Mackey, Aaron
  13. Developed by
    Roos, David S., Ph.D.
  14. Developed by
    Brunk, Brian P., Ph.D.
  15. Developed by
    Chakravarthula, Praveen
  16. Developed by
    Gao, Jerric (Xin)
  17. Developed by
    Fischer, Steve
  18. Developed by
    Treatman, Charles
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2013-03-21T14:43:49.599-04:00
  4. creator
    fcoldren
  5. modified
    2013-03-22T14:25:45.529-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016