VMD-L Mailing List

From: Elijah Roberts (erobert3_at_scs.uiuc.edu)
Date: Tue May 22 2007 - 16:01:53 CDT

Hi Armen, when we create BLAST databases we usually use a command like this:

formatdb -i uniprot_sprot -o T

The key is the -o T option which tells formatdb to build the index files
so that MultiSeq can retrieve the sequence data from the database.

Elijah

Armen Nalian wrote:
> 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/