[BiO BB] How to align whole query sequence with blast
stefanielager at gmail.com
Fri Nov 18 03:30:41 EST 2005
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 sequences.
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:
> 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 - BiO_Bulletin_Board at bioinformatics.org
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