This is the Linux app named COGsoft to run in Linux online whose latest release can be downloaded as COGsoft.04.19.2012.tgz. It can be run online in the free hosting provider OnWorks for workstations.
Download and run online this app named COGsoft to run in Linux online with OnWorks for free.
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- 1. Downloaded this application in your PC.
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COGsoft to run in Linux online
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DESCRIPTION
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)
Audience
Science/Research
User interface
Command-line
Programming Language
C++
This is an application that can also be fetched from https://sourceforge.net/projects/cogtriangles/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
