[Bioperl-l] best way to map ESTs to genomic seq: blastn?
qfdong at iastate.edu
Mon Feb 24 11:17:54 EST 2003
Another choice is to use GeneSeqer program, which performs spliced alignment
of Genomic seq vs. ESTs (or cDNAs, or proteins). For more information, you can
check out its webserver at www.plantgdb.org/cgi-bin/GeneSeqer.cgi Or its
specialized server for mapping ESTs onto the Arabidopsis genome at
> We use Jim Kent's "blat" in cDNA=>genome mode. It is slightly less
> than blastn, but avoids many of the latter's artefacts, such as additional
> bases at the ends of the boundaries.
> On Monday 24 February 2003 12:03 pm, Charles Hauser wrote:
> > All,
> > I'd like to map a set of ESTs to genomic sequence and was planning to
> > just blastn EST vs genomic - I'd like to find the 'best' scaffold hit(s)
> > for each EST.
> > I am not sure how to pair HSPs for a given EST when they span an intron.
> > Is there a better methodology?
> > Chuck
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> Lincoln D. Stein Cold Spring Harbor Laboratory
> lstein at cshl.org Cold Spring Harbor,
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
Qunfeng Dong, Ph.D
2104 Molecular Biology Building
Iowa State University
Ames, IA 50010
More information about the Bioperl-l