[BiO BB] How to align whole query sequence with blast

Ryan Golhar golharam at umdnj.edu
Fri Nov 18 10:08:46 EST 2005

Alternatively, you can use Splign or Spidey from NCBI...

-----Original Message-----
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. 
PMID: 15728110 
Slater GS, Birney E. 
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31. 
PMID: 15713233

On 11/18/05, Evgeny Cheremushkin <cher at biorainbow.com> wrote: 

Hello bio_bb,

I  want to align whole query sequence onto genome with blast
(not only a part of query sequence). Is there any option for 

Best regards,
Evgeny Cheremushkin,
BioRainbow Group,
phone:  +7 (383) 3306470
mobile: +7 (913) 8916858
e-mail: cher at biorainbow.com
web: http://www.biorainbow.com

Bioinformatics.Org general forum  -
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