[Bioclusters] Web BLAST

[Arshad Khan]

We do that every day. I havent checked lately the blast version but it ought
to be 2.2x. which ought to suffice your needs. Databases at NCBI are the
same ones that they use themselves and its not 5 years old. Infact its
updated on daily basis as new data becomes available. What we do is that we
download all finished bacterial genome data from genbank and unfinished
bacterial genomes database from different sequencing centers like TIGR. Give
all the genomes our own UIDs (Unique ID), run formatdb etc. It all works
quite well. Except sometimes you will find that the new wwwblast (esp.
blastx) will throw up problems when you paste short sequences (< 50). At
genbank (NCBI) you will find flat files in fasta format already. Unless you
want to give your own UIDs to the files like we do you dont need to do
anything to those files except run formatdb.
check out http://vge.ac.uk to see how it all works for us.

Arshad
Bacterial Pathogenesis & Genomics Unit
Department of Immunity & Infection
Medical School
University of Birmingham
tel: 0121 414 2859
----- Original Message -----
From: "Jeremy Mann" <jeremy@bioc09.v19.uthscsa.edu>
To: <bioclusters@bioinformatics.org>
Sent: Wednesday, November 20, 2002 3:13 PM
Subject: Re: [Bioclusters] Web BLAST


>
> > Hi Jeremy,
> > I have been running a wwwblast server for more than a year now. Here is
> > what you need to add in blast.rc.
> > blastn     dna files
> > blastp     protein files
> > blastx     protein files
> > tblastn    dna files
> > tblastx    dna files
> >
> > The rest is quite simple but let us know if you have any more problems?
>
> Just a couple more questions..... Another researcher looked over the
> installation and did a couple BLAST runs. According to him, the blast that
> comes with wwwblast is pretty old and the databases are formatted to what
> NCBI used 5 years ago. Does NCBI use the same databases as what they
> release to us?
>
> If the database continues to be a problem, we also have the complete GCG
> database available. Since BLAST wants its database in its own format, how
> hard would it be to take the flat files from Genbank, format to FASTA,
> then format to NCBI (using formatdb)? Or is this even possible?
>
>
>
> --
> Jeremy Mann
> jeremy@biochem.uthscsa.edu
>
> University of Texas Health Science Center
> Bioinformatics Core Facility
> Phone: (210) 567-2672
>
>
>
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