[Bioperl-l] blastz parser

Jason Stajich jason at cgt.duhs.duke.edu
Fri Apr 16 16:08:08 EDT 2004

Karen -

You can convert the blastz lav output to axt or psl with Jim Kent's
lavToPsl or lavToAxt.

Bio::SearchIO can parse psl or axt, Bio::Tools::Blat can also parse psl
output. (I think there is an off-by-one error in SearchIO::psl that Elliot
M reported but it hasn't been fixed yet).

On Fri, 16 Apr 2004, Karen Hayden wrote:

> Hello all,
>     Is there a module to parse blastz output?
> Thanks,
> Karen

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

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