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

[Leonardo Marino-Ramirez]

Chuch, I have used spidey, an mRNA-to-genomic alignment program. See
http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/Spidey/

But you need to know which genomic contig contains your EST.

Leonardo

> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org 
> [mailto:bioperl-l-bounces at bioperl.org] On Behalf Of Charles Hauser
> Sent: Monday, February 24, 2003 12:03 PM
> To: BioPerl-List
> Subject: [Bioperl-l] best way to map ESTs to genomic seq: blastn?
> 
> 
> 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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