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OrthoMCL

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013a-bda8-e2f3-d69a-d90d80000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Resource Description
    "To distinguish functional redundancy from divergence, this method identifies “recent” paralogs to be included in ortholog groups as within-species BLAST hits that are reciprocally better than between-species hits. This approach is similar to INPARANOID, but differs primarily in the requirement that recent paralogs must be more similar to each other than to any sequence from other species. To resolve the many-to-many orthologous relationships inherent in comparisons across multiple genomes, OrthoMCL applies the Markov Cluster algorithm (MCL; Van Dongen 2000; http://micans.org/mcl/), which is based on probability and graph flow theory and allows simultaneous classification of global relationships in a similarity space. MCL simulates random walks on a graph using Markov matrices to determine the transition probabilities among nodes of the graph. The MCL algorithm has previously been exploited for clustering a large set of protein sequences, where it was found to be very fast and reliable in dealing with complicated domain structures (Enright et al. 2002). OrthoMCL generates clusters of proteins where each cluster consists of orthologs or “recent” paralogs from at least two species." OrthoMCL was developed jointly with Mark Heiges and Ryan Thibodeau from the <b>Center for Tropical & Emerging Global Diseases, University of Georgia</b>.
  2. Used by
    Computational Biology and Informatics Laboratory
  3. Version
    2.0
  4. Operating System
    UNIX
  5. Operating System
    Web based
  6. Data Input
    Proteins
  7. Data Output
    Ortholog groups
  8. Data Output
    Paralog pairs
  9. Data Output
    Paralog groups
  10. Software purpose
    Protein sequence classification objective
  11. Software purpose
    Clustering analysis objective
  12. Related Publication or Documentation
    OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
  13. Website(s)
    http://genome.cshlp.org/content/13/9/2178.full
  14. Website(s)
    http://orthomcl.org/common/downloads/software/
  15. Website(s)
    http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi
  16. Related Technique
    Bioinformatics analysis
  17. Developed by
    Stoeckert, Christian J., Jr., Ph.D.
  18. Developed by
    Li, Li, Ph.D.
  19. Developed by
    Chen, Feng, Ph.D.
  20. Developed by
    Fischer, Steve
  21. Developed by
    Iodice, John
  22. Software license
    GNU General Public License
  23. Algorithm used
    Markov Cluster algorithm
  24. Coded in
    Perl
 
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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016