VMD-L Mailing List

From: John Eargle (eargle_at_uiuc.edu)
Date: Fri May 18 2007 - 14:02:09 CDT

What, if any, error messages are you getting when you try to run BLAST?

You could try to run blastpgp standalone to see if the problem is in MultiSeq or not. This is the default, non-profile BLAST command being run by MultiSeq:
blastpgp -d <database> -e 5.0 -i <inputFilename> -o <outputFilename> -m 6 -b 500 -j 1

~John Eargle

---- Original message ----
>Date: Fri, 18 May 2007 12:29:41 -0500
>From: Armen Nalian <nalianarmen_at_sfasu.edu>
>Subject: Re: vmd-l: custom db in Multiseq
>To: eargle_at_uiuc.edu
>Cc: vmd-l_at_ks.uiuc.edu
>
> Sequences are in fasta format. I usually run
> formatdb -i mysequences.fasta -p T -n myDB.
> I was wondering what additional parameters are
> required for blast in multiseq. In multiseq blast
> against uniprot_sprot works fine, but when I select
> myDB, blast fails.
> Thank you,
> Armen
>
> John Eargle wrote:
>
> It depends on how your sequence data is formatted. Help with formatdb is available here: http://web.csb.ias.edu/blast/formatdb.txt
>
> ~John Eargle
>
> ---- Original message ----
>
>
> Date: Thu, 17 May 2007 18:48:01 -0500
> From: Armen Nalian <nalianarmen_at_sfasu.edu>
> Subject: vmd-l: custom db in Multiseq
> To: vmd-l_at_ks.uiuc.edu
>
> Hello,
> I would like to use a custom database for blast search in Multiseq. How
> can I format a sequence file? What arguments are required for formatdb?
> Thank you,
> Armen
>
>
>
>
>
> --
> Armen Nalian
>
> Research Associate
> Department of Biotechnology
> Stephen F. Austin State University
> E-mail: nalianarmen_at_sfasu.edu
> Tel: 936-468-6931
> Cell: 936-615-2563
>
> Science Research Center
> P.O Box 6132-SFA Station
> Nacogdoches, Texas 75962-3006