From: Armen Nalian (
Date: Fri May 18 2007 - 12:29:41 CDT

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,

John Eargle wrote:
It depends on how your sequence data is formatted.  Help with formatdb is available here:

~John Eargle

---- Original message ----
Date: Thu, 17 May 2007 18:48:01 -0500
From: Armen Nalian <>  
Subject: vmd-l: custom db in Multiseq  

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 Nalian
Research Associate 

Department of Biotechnology
Stephen F. Austin State University

Tel: 936-468-6931
Cell: 936-615-2563

Science Research Center
P.O Box 6132-SFA Station
Nacogdoches, Texas 75962-3006