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Identifying 11,500 cDNA orthologs


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#1 tpow

tpow

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Posted 12 August 2009 - 11:39 AM

The good people at bioforums,

My goal is to identify orthologous cDNA contigs between two Xenopus species. I have a list of 11,500 cDNA genbank accession id's for the laevis species and I need to identify the orthologous cDNA accession IDs in the tropicalis species. Furthermore, I need to look at the alignment of the two sequences, and determine if their overlapping regions are short in the 3' or 5' end.

Clearly, the very long way to do this would be to individually BLAST each laevis cDNA sequence to find the ortholog. I'm certain that there are methods to automate this process, and I a would be forever grateful if someone could provide tips on how to speed up this mundane process.

Thank you very much!




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