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data mining with blastp

Everything on bioinformatics, the science of information technology as applied to biological research.

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data mining with blastp

Postby corleyma » Fri Jun 11, 2010 7:21 pm

Hey guys,

I have a very particular task I am trying to accomplish using blastp, and after searching and reading thousands of things about the particulars of BLAST and associated tools, I am no closer to finding an easy way to automate what should be a simple process. Here's what I am trying to do:

I have a query protein sequence from a reference taxon that I need to blastp against the nr database multiple times, each time restricting the query to a particular taxid, taking the number 1 hit and collecting the sequence information in FASTA format. So, what I want to do is some kind of bastardized batch blastp, blasting one sequence against multiple species and getting the sequences of the best matches for each species aggregated in a single file in FASTA format.

Do any of you have a clue as to how to proceed? If there's software to download/buy, I am not opposed to that - but freeware/opensource solutions are preferred.

Thanks,
Matt
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Postby JackBean » Fri Jun 11, 2010 8:45 pm

how many taxons you need to check?

Do you know programming?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby fcs » Wed Aug 11, 2010 3:58 am

The company that I work for may have a tool that can do the job but before I suggest it, I will need to know how many taxons you are planning on blasting.
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