[Bioclusters] standalone blast server problem

Khan, Arshad bioclusters@bioinformatics.org
Thu, 27 Mar 2003 10:48:29 -0000


I had the same problem recently, download the latest blastserver from ncbi
ftp://ftp.ncbi.nih.gov/blast/server/wwwblast_Feb.10.2003/. There was a limit
to the total length of databases names you could add in blast.rc in versions
prioir to Jun 2002. If the problem persists than have multiple entries of
the blast program in blast.rc ie. add blastp newdata on another line. Hope
this helps. 

Arshad Khan
Pathogenesis and genomics unit
Division of Immunity & Infection
Medical School
University of Birmingham
Edgbaston, B15 2TT

-----Original Message-----
From: Jeremy Mann [mailto:jeremy@bioc09.v19.uthscsa.edu]
Sent: 26 March 2003 21:27
To: bioclusters@bioinformatics.org
Cc: yuyu.bai@syngenta.com
Subject: Re: [Bioclusters] standalone blast server problem

> We downloaded a standalone blast web server from NCBI website last year.
> It has been working fine until very recently. A few new datasets with
> long names
> were added into the directory where we have all the blastable datasets.
> After that, blastn
> works for some datasets and all other types of blast search don't work.
> If I remove these long-name
> datasets, everything would work. There are no strange characters in
> these names except
> a few have '+' sign in the name. The problem doesn't go away if I only
> remove the ones with '+' sign.
> These long-name datasets themselves work ok for blastn search. The
> problem is that their existence interfere
> with normal function of other datasets.
> If you know the cause of this problem. Please help, many thanks.
> Yu-yu

If your using the preformatted datasets, then you'll need to update to the
2.2.5 of the BLAST binaries since they are introducing a slightly new
format to the databases. I think this is what your experiencing.

Jeremy Mann

University of Texas Health Science Center
Bioinformatics Core Facility
Phone: (210) 567-2672

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