[Bioclusters] Web BLAST

[Eric Engelhard]

On Tue, Nov 19, 2002 at 01:04:28PM -0600, Jeremy Mann wrote:
> I am trying to get the wwwblast databases installed. I have downloaded
> the Preformatted Databases and am having trouble with the blast.rc file.
> I am not a scientist, so I do not know which databases need to be
> searched with blastn, blastp, tblast and so forth. If anybody can send
> me their blast.rc file, I would be greatly appreciated.

Hello Jeremy,

I've not set up wwwblast in a while and I don't have a copy of
either the blast.rc or the html files, but it is pretty simple:

blastn: blast _n_ucleic acid sequence against nucleic acid reference
database. This would be the nt, gss, htg, patent, and est (or related
species specific databases.

blastp: blast _p_protein sequences against protein databases. This
would be nr, swissprot, etc.

blastx: nucleic acid sequence against protein database (nr, swissprot,
etc.)

tblastn :protein sequence against nucleic acid database (see blastn
reference dbs)

tblastx: nucleic vs nucleic (program translates both to protein
sequence but you want nucliec acid databases as for blastn)

Be sure that the blast.rc and html doc reflect the same databases.

Also, there is a nice little blast tutorial which covers the
databases:
http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/query_tutorial.html

Good luck,

Eric

-- 
Eric Engelhard - www.cvbig.org - www.appliedgenex.com