[Bioperl-l] Can I use BLAST against a database like MySQL

Hubert Gaynor hubert.gaynor at yahoo.com
Thu Apr 17 20:53:16 EDT 2008


Hi Sean,

I got it. Thank you so much!

Hubert

----- Original Message ----
From: Sean Davis <sdavis2 at mail.nih.gov>
To: Hubert Gaynor <hubert.gaynor at yahoo.com>
Sent: Thursday, April 17, 2008 6:36:02 PM
Subject: Re: [Bioperl-l] Can I use BLAST against a database like MySQL

On Thu, Apr 17, 2008 at 2:19 AM, Hubert Gaynor <hubert.gaynor at yahoo.com> wrote:
> Hi,
>
>  As far as I know, before using BLAST to do the alignment the first thing should be done is typing formatdb to construct a database. But I was wondering whether it is possible to construct a database with MySQL which probably will grant the BLAST search a higher speed and make the database management much easier?
>

formatdb is used to make a representation that can be used efficiently
by blast.  That representation already makes blast faster.  MySQL
can't be used for such things.  As for speeding blast, if you have a
multiprocessor machine, you can take advantage of those using blast
and increasing the number of processors.  Also, while blast is a very
versatile program, it is not the only alignment program available.
Depending on your needs, you could look at other programs such as blat
or gmap that can be 2-3 orders of magnitude faster than blast.

Sean






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