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orthomclRemoveIdenticalGroups

By Roos D., Last update 1494698999
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orthomclRemoveIdenticalGroups description

OrthomclRemoveIdenticalGroups produces a groups file that has had removed from it those groups that are identical in a second, reference, groups file. OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species or genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog or recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org or 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.


Parent program: orthomcl

OrthoMCL allows automatic identification of orthologous groups. The OrthoMCL uses NCBI reciprocal (one-to-one) BLAST and Markov clustering algorithms in conjunction with a relational database (MySQL) to store the intermediate data. OrthoMCL produces results similar to INPARANOID when applied to two genomes. OrthoMCL differs from the EGO strategy and the COG algorithm commonly applied to prokaryotic genomes and allows an improved recognition of 'recent' paralogs.