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

[Lincoln Stein]

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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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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