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Software to identify orthologs


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#1 fhsantanna

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Posted 28 July 2010 - 04:42 PM

Hi.
Does somebody know a good program to orthologs identification? I found one named RSD (http://roundup.hms.h.../site/index.php), however it requires the wu-blast2 software, which is not available anymore in its site (http://blast.wustl.edu/).

Thanks.

#2 z1dane

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Posted 10 August 2010 - 01:14 AM

Hi.
Does somebody know a good program to orthologs identification? I found one named RSD (http://roundup.hms.h.../site/index.php), however it requires the wu-blast2 software, which is not available anymore in its site (http://blast.wustl.edu/).

Thanks.


Hello,

You can come up with your own definition of what an ortholog is. For example, a reciprocal best hit is usually used. You can download your own copy of BLAST from NCBI (ftp://ftp.ncbi.nih.gov/blast/), download the genomes and prepare BLAST database files. Say you wanted to look for mouse orthologs in rat. You would BLAST the gene of interest to rat. If you find one best scoring match, use that match to BLAST back to mouse. If the best scoring match in rat is the best scoring match in mouse, you can define it as an ortholog.

Hope that helps,

z




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