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  1. OrthoMCL (View Publication)
    Full Name of the Resource : Orthologous protein clusters from multiple genomes
    Resource Category : Databases -> General Genomics Databases

    Brief Description : The OrthoMCL database houses a comprehensive collection of ortholog groups automatically assigned by applying the OrthoMCL algorithm to wide variety of complete genomes, spanning the tree of life. Each ortholog group consists of orthologs from different species, combined with recent paralogs (in-paralogs) from same species. The current release incorporates complete genomes for 55 species, including 16 bacterial and 4 archaeal species representing phylogenetically diverse lineages, and most of the currently available complete eukaryotic genomes: 24 unikonts (12 animals, 9 fungi, the microsporidian, Encephalitozoan, Dictyostelium, Entamoeba), 4 plants/algae, and 7 species of apicomplexan parasites. 511,797 proteins (81.6% of the total dataset) were clustered into 70,388 ortholog groups, and this ortholog dataset may be queried based on keyword descriptions, BLAST similarity, or specified protein names or group accessions numbers. Ortholog groups exhibiting specific phyletic patterns may also be identified, using either a graphical interface or a text-based Phyletic Pattern Expression grammar. Such studies hold out great promise for drag target identification. OrthoMCL-DB will be updated twice a year, as additional genome sequencing projects progress to completion.
    Subject Area : Protien Cluster


    Institute/s :
    Departments of Biology and Chemistry, Center for Bioinformatics, and Penn Genomics Institute, University of Pennsylvania, Philadelphia PA 19104, USA
    Country : United States

    Associated Institutes :

    • Departments of Chemistry, Biology and Genetics, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania Philadelphia, PA 19104-6018, USA

    Associated Country : USA


    Authors/Contributors : Chen F; Mackey A.J; Stoeckert C.J Jr; Roos D.S.
    Contact Email : orthomcl@pcbi.upenn.edu
    Year : 2006

    Keywords : Animals; Cluster Analysis; *Databases, Protein; *Genomics; Internet; *Phylogeny; Proteome / *classification / genetics; *Sequence Homology, Amino Acid; User-Computer Interface