[BioRuby] Best way to do homology search

Toshiaki Katayama k at bioruby.org
Tue May 9 20:37:14 UTC 2006


On 2006/05/10, at 2:18, Kfir Lavi wrote:

> Hi,
> I have sql database with table of dna sequences.
> I would like to do homology search on the table.

How do you plan to execute homology search against SQL database?

BioRuby can parse the result of BLAST, FASTA etc. commands
and these are usually performed for the FASTA formated sequence file.
I think some of these programs support to run against SQL database directly,
but I have never tried by myself.
If the result formats are same in both way (flatfile DB and sql DB),
you can use BioRuby parser to extract % similarity.


> A user enter a sequence and the return is sequences with the
> percentage of similarity.
> Is there a simple function to use or I have to put some code together?
> I have read the Tutorial.rd but need more help.
> Thanks,
> Kfir
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