[Bioperl-l] longest ORF

[Brian Osborne]

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

--
_____________________________________________________________   .`.`o
                                                         o| ,\__ `./`r
  Dan Kortschak    kortschak@rsbs.anu.spanner.edu.au     <\/    \_O> O
                                                          "|`...'.\
  Before you criticise a man, try to walk a mile in his    `      :\
  shoes. Then, if he doesn't like what you have to say,           : \
  you'll be a mile away, and you'll have his shoes.               :  \

  The address above will not work, remove the spanner from the works.

By replying to this email you implicitly accept that your response may
be forwarded to other recipients.
Permission is granted for fair use reproduction.

_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l