Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.
Features
- A description of strengths/weaknesses of different methods: Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Computational methods for Gene Orthology inference. Brief Bioinform. 2011 Sep;12(5):379-91. Epub 2011 Jun 19. http://www.ncbi.nlm.nih.gov/pubmed/21690100
- Algorithm reference: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics. 2010 Jun 15;26(12):1481-7. Epub 2010 May 2. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq229?ijkey=zD7TIWnncGvDGYE&keytype=ref
- Good/thorough review of orthologs/COGs: Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 2005;39:309-38. http://www.ncbi.nlm.nih.gov/pubmed/16285863
- Original COG paper: Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997 Oct 24;278(5338):631-7. http://www.ncbi.nlm.nih.gov/pubmed/9381173
- COG database: Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000 Jan 1;28(1):33-6. http://www.ncbi.nlm.nih.gov/pubmed/10592175
- Koonin lab webpage site: http://www.ncbi.nlm.nih.gov/research/groups/koonin/
- Official FTP site: ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/ (although at the moment, the readme just points to the sourceforge page)
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User Reviews
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For building your own groups of orthologous genes (if you don't know what that is, this is not for you:). Note: if all you want is data about orthologs, you are better off looking elsewhere (such as http://www.ncbi.nlm.nih.gov/COG/).