[Bioperl-l] best way to map ESTs to genomic seq: blastn?

[Qunfeng Dong]

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 
www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi

Regards,

Qunfeng


 
> We use Jim Kent's "blat" in cDNA=>genome mode.  It is slightly less 
sensitive 
> than blastn, but avoids many of the latter's artefacts, such as additional 
> bases at the ends of the boundaries.
> 
> Lincoln
> 
> 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
> >
> >
> >
> >
> > _______________________________________________
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> > Bioperl-l at bioperl.org
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> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, 
NY
> ========================================================================
> 
> 
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Qunfeng Dong, Ph.D
ZmDB Manager 
2104 Molecular Biology Building
Iowa State University
Ames, IA 50010