[BiO BB] [Fwd: Small Genome Similarity]

[Iddo Friedberg]

Generally, the strategy should be to look for homology in the translated 
regions, using the protein amino-acid sequence. Protein sequences are 
much less "noisy" than the DNA sequences coding them, so using a protein 
sequence your search sensitivity is  enhanced.
Furthermore, you have better software to match distantly similar 
sequences using protein sequences, starting at PSI-BLAST and moving up 
to such stuff as 3D-PSSM, FFAS03, etc.

Hope this gets you on the right track.

Iddo

J.W. Bizzaro wrote:
> Please CC reply to <t.fiedler at umiami.edu>.  Jeff
> 
> 
> ------------------------------------------------------------------------
> 
> Subject:
> Small Genome Similarity
> From:
> "Tristan Fiedler" <t.fiedler at umiami.edu>
> Date:
> Thu, 12 Feb 2004 19:19:42 -0500 (EST)
> To:
> Mailman-owner at bioinformatics.org
> 
> 
> Dear BIO,
> 
> Could you please post the following to the most suitable discussion group
> within bioinformatics.org ?  Thank you kindly in advance.
> 
> ##########################
> I am looking at a novel 2.4 KB viral genome and want to see if anything
> homologous is known.
> 
> Have tried blastn,blastx variants but nothing comes up (possibly due to
> frame or simply divergence).
> 
> This beastie may replicate in the mitochondria of vertebrates so
> translations may need to use mito not nuclear codons.
> 
> Please let me know if you have any suggestions or experience looking at
> similar sequences.
> 
> Thank you,
> 
> Tristan
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo