[Bioperl-l] HOWTO Beginners: formatdb program/indexing a databasesequence file?

Ryan Golhar golharam at umdnj.edu
Mon Oct 17 16:11:07 EDT 2005

db.fa is a fasta file containing the sequences you want to make a
blast'able database out of.

formatdb is a program that comes with BLAST or the NCBI Toolkit.  You
need to download it from NCBI.  

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sam
Sent: Monday, October 17, 2005 3:41 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] HOWTO Beginners: formatdb program/indexing a
databasesequence file?

Under the BLAST section, the Beginners HOWTO
(http://bioperl.org/HOWTOs/html/Beginners.html  ) says
"The example code assumes that you used the formatdb program to index
the database sequence file "db.fa"."
Could someone tell me who to go about creating the db.fa file.  looked
on the webiste but there was no reference to a formatdb program.   
My goal is:  I have a gene sequence and I want to align it again the
chromosome sequence, both are fasta format.  Can I do this with the
blast program on my own computer?  
Thank you in advance. 

Sam Al-Droubi, M.S.
saldroubi at yahoo.com _______________________________________________
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