[BioPython] Re: BioPython digest, Vol 1 #297 - 1 msg

[Scott T. Kelley]

Thanks for the message and ideas Brad. The tblastn idea was the first one I
thought of but it was so slow as you said. It didn't occur to me to use
download the databases locally! We have a good deal of hard drive space so
that will not be a problem.

Thanks for the quick response and ideas.

Cheers! -Scott


>
> Message: 1
> Date: Sat, 13 Oct 2001 14:28:03 -0400
> From: Brad Chapman <chapmanb@arches.uga.edu>
> To: biopython@biopython.org
> Subject: Re: [BioPython] retrieving mRNA using protein sequence
>
> Hi Scott;
>
> > I was wondering if anyone out there might have some advice on how I
might
> > best go about retrieving DNA sequence using the translated protein.
>
> I think a relatively easy way to do this is to use tblastn (protein
> query against a translated database in all 3 frames). For instance,
> querying your example sequence against the nr database gives me my
> guess for the identity of the original mRNA:
>
> >gi|516327|emb|X80070.1|DMUSVAR39 D.melanogaster mRNA for Su(var)3-9
> protein
>
> Provided your sequences are in public databases, you can use use
> biopython code to automate BLASTing against NCBI, parsing the BLAST
> report, and fetching the original sequence. This is probably only
> feasible if you have a small number of original sequences to find
> out the identity of. tblastn is both slow (it took 5 minutes for a
> Saturday afternoon blast of your query) and hard on NCBI resources.
>
> If you have a ton of sequences to find the identity of, the best
> thing to do would be to set up a local database of potential mRNA
> sequences (if you can narrow this down to something less than all of
> nr, this would also save a lot of time!), and use local blast
> against this database. You could also use biopython to automate
> doing everything here as well.
>
> Hope this helps, and thanks for the kind words about the documentation :-)
>
> Brad
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