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

[Barry Moore]

Sam-

You can run blast on your own computer.  formatdb is a program that
comes with the blast distribution that formats sequences in a fasta file
into a blast database for use in blast searches.  If you have installed
BLAST locally, then you have formatdb.  Documentation for formatdb is
found with man formatdb on a linux system, or here for an online source:
ftp://ftp.ncbi.nih.gov/blast/documents/

The db.fa file is any fasta file that you want to create a blast
database out of with formatdb.

A couple of your questions suggest that you would greatly benefit from
exploring the UCSC genome browser at http://genome.ucsc.edu/.  In this
case you have a gene sequence that you want to align to a genome.  BLAST
will get you started, but you're better off with BLAT for that job.  If
you're doing this for one of the many genomes covered in the UCSC genome
browser, then they've probably already done this for you.  If you're
doing it for something new or for a lot of genes then you can run BLAT
locally, and Bioperl can help you with the that:

Bio::Tools::Run::Alignment::Blat.html
Bio::Tools::Blat.html

Barry

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sam
Al-Droubi
Sent: Monday, October 17, 2005 1:41 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] HOWTO Beginners: formatdb program/indexing a
databasesequence file?

All,
 
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. 
 


Sincerely, 
Sam Al-Droubi, M.S.
saldroubi at yahoo.com
_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l