[Bioperl-l] longest ORF

Brian Osborne brian_osborne@cognia.com
Tue, 30 Jul 2002 08:15:53 -0400


Dan,

Take a look at Bio::PrimarySeqI.pm for the full description of translate(),
it can take a frame argument. Jason wrote a script that uses translate() to
its fullest extent, it's called scripts/make_mrna_protein.pl. It may not be
exactly what you want but it shows how one can use translate().

Brian O.


-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Dan Kortschak
Sent: Monday, July 29, 2002 7:55 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] longest ORF

Hi All, I'm looking to see if anyone has a small script to take a Bio::Seq
object and find the longest ORF ((+) strand or both strands).
Altenatively, is there an easy way to do this using Bio::Seq (translate
doesn't seem to take a frame for translation so I'm guessing that it
translates in frame 1 - is this right?)

thanks
Dan Kortschak

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