[BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #640 - 1 msg
hk_soni2003
hk_soni2003 at indiatimes.com
Fri Feb 20 06:44:48 EST 2004
bio_bulletin_board at bioinformatics.org wrote:
When replying, PLEASE edit your Subject line so it is more specific
than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any
unrelated text from the body.
Today's Topics:
1. Re: [Fwd: Small Genome Similarity] (Martin Gollery)
--__--__--
Message: 1
Date: Wed, 18 Feb 2004 16:45:52 -0800
From: Martin Gollery
To: bio_bulletin_board at bioinformatics.org
Cc: t.fiedler at umiami.edu
Subject: Re: [BiO BB] [Fwd: Small Genome Similarity]
Reply-To: bio_bulletin_board at bioinformatics.org
Tristan,
Try going to Blosum30 for the matrix, and lower the open and extend gap
penalties, and lower the reporting threshold. Use the mito codons. If you still
don't get hits, switch from BLAST to Smith-Waterman, or use Interproscan to
compare it to several signature databases.
Marty
Quoting "J.W. Bizzaro" :
>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
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
-------------------------------------------------
This mail sent through https://webmail.unr.edu
--__--__--
_______________________________________________
BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
End of BiO_Bulletin_Board Digest
Indiatimes Email now powered by APIC Advantage. Help!
HelpClick onthe image to chat with me
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bbb/attachments/20040220/9bc43381/attachment.html>
More information about the BBB
mailing list