[Bioperl-l] aa -> dna alignment (was: help with Bioperl)

Jason Stajich jason at cgt.duhs.duke.edu
Sun Feb 22 14:52:10 EST 2004

Not directly - you can use genewise or Guy Slater's exonerate with the
protein2dna model and then use Bioperl parsers to parse these reports.

You can also use BLAT, TBLASTN, TFASTY but you may have to cleanup these
alignments some.

Genewise should give the most accurate alignments but can be slow if you
don't already know about where your gene should land in the genomic

On Sun, 22 Feb 2004, Parvesh wrote:

> Hi All, IS there a method in Bioperl to map the amino acid exon
> structure to the genomic sequence?
> Could you help me to locate this and help me to explain how to use it ? Thanks very much for your help.
> Best wishes
> parvesh

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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