[BiO BB] How to align whole query sequence with blast
golharam at umdnj.edu
Fri Nov 18 10:08:46 EST 2005
Alternatively, you can use Splign or Spidey from NCBI...
From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
] On Behalf Of Stefanie Lager
Sent: Friday, November 18, 2005 3:31 AM
To: Evgeny Cheremushkin; The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] How to align whole query sequence with blast
If you want to align cDNA or proten sequences to genomic DNA it's better
to use the algorithms GMAP http://www.gene.com/share/gmap or Exonerate
http://www.ebi.ac.uk/~guy/exonerate/ instead of BLAST . These two
algorithms are faster then blast, and they are made to handle introns.
Wu TD, Watanabe CK.
GMAP: a genomic mapping and alignment program for mRNA and EST
Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005 Feb 22.
Slater GS, Birney E.
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31.
On 11/18/05, Evgeny Cheremushkin <cher at biorainbow.com> wrote:
I want to align whole query sequence onto genome with blast
(not only a part of query sequence). Is there any option for
phone: +7 (383) 3306470
mobile: +7 (913) 8916858
e-mail: cher at biorainbow.com
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