Download
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)
Categories
Bio-InformaticsLicense
Public DomainFollow COGsoft
Other Useful Business Software
MongoDB Atlas runs apps anywhere
MongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
Rate This Project
Login To Rate This Project
User Reviews
-
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/).