[BiO BB] [Fwd: Small Genome Similarity]

[val]

Yes, seemingly right, but a protein-expression machinery
depends as well on local translation env, and may send mixed
messages about the DNA features.  So, the homologies - yes,
but what they indicate? Right?
cheers,
val

----- Original Message -----
From: "Iddo Friedberg" <idoerg at burnham.org>
To: <bio_bulletin_board at bioinformatics.org>; <t.fiedler at umiami.edu>
Sent: Saturday, February 14, 2004 11:11 PM
Subject: Re: [BiO BB] [Fwd: Small Genome Similarity]


>
>
> 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
>
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