URL: http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi
Proper Citation: OrthoMCL DB: Ortholog Groups of Protein Sequences (RRID:SCR_007839)
Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. OrthoMCL starts with reciprocal best hits within each genome as putative in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as putative ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.
Synonyms: OrthoMCL DB
Resource Type: data or information resource, database
Keywords: FASEB list
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