[Bioperl-l] public qblast servers?

[Cook, Malcolm]

Russell,

I don't think anyone but NCBI implements the qblast protocol.

However, much of the sequences at wormbase for nematode are submitted to genbank.  So, you simply need to figure out the appopriate combination or organism, database, and entrez query that corresponds to the dataset you want to query.  Also, you should know, that Vector NTI gives you a list of ncbi databases from which to choose.  But his list is incomplete.  You can type into this box any database listed here: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html and it works

So, for example, to blast against c elegans refseq mrnas, you would provide refseq_mrna as the database and 'Caenorhabditis elegans' as the organism.

Of course many other combinations are possible. This should work for nematode and elegans data.  H contortus appears not yet released to genbank, so I think you will have to download them and build your own blast database for use with your qblast wroapper.

Regarding your faked qblast, would you be willing to share this code with our non-profit research institute?  I'm in a similar position and have planned to write a fake qblast wrapper but have not made the time.....  I, and many researchers here, would be obliged.

Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
Sent: Tuesday, July 08, 2008 9:37 PM
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] public qblast servers?

Hi all,
Not a BioPerl question, but does anyone know of any public qblast servers?
DB's of interest would be at:

                Wormbase:  http://www.wormbase.org/
                Nematode Net:  http://www.nematode.net/
                H. contortus:
http://www.sanger.ac.uk/Projects/H_contortus/

We have a script that fakes qblast internally so Vector NTI will work with it but some of our users would like to blast elsewhere.

Thanx,

Russell Smithies

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