[Bioperl-l] ORF FInder

[Brian Osborne]

Lynn,

Jason is also saying that you can use EMBOSS programs from within Bioperl.
Here's an example using EMBOSS's getorf program :

use Bio::SeqIO;
use Bio::Factory::EMBOSS;

$factory = new Bio::Factory::EMBOSS;
$app = $factory->program("getorf");
%input = ( -sequence => "input.fasta", -minsize => 22, -outseq =>
"orfs.fasta" );
$app->run(\%input);
$seqio = Bio::SeqIO->new(-file => "orfs.fasta");
$seqobj = $seqio->next;

Or something....

True, it's not strictly Bioperl-ish but you have tremendous amount of
functionality in the EMBOSS suite, and this makes it all available easily.
My understanding is that the EMBOSS modules will return Bioperl objects
someday, rather than just create files for you as in the example above. To
get the positions of the ORFs you're going to have parse the
header/description line yourself, it's provided by the Seq object's desc()
method.

I'll add this to the new FAQ, something about functionality not found in
Bioperl might be found in EMBOSS, which is accessible through Bioperl.

Brian O.


----- Original Message -----
From: "Jason Stajich" <jason@cgt.mc.duke.edu>
To: "Lynn Stevens" <lynn_m_stevens@hotmail.com>
Cc: <bioperl-l@bioperl.org>
Sent: Sunday, February 10, 2002 3:04 PM
Subject: Re: [Bioperl-l] ORF FInder


> Not in bioperl directly but you can use emboss's getorf program.
>
> On Sun, 10 Feb 2002, Lynn Stevens wrote:
>
> > Is there a module in BioPerl which allows you to take a sequence and get
> > back a list of all the ORFs (or even just the largest ORF) in all six
frames
> > (or even just one frame) indexed by sequence position.
> >
> > In other words you would submit a seq object and you would get back a
set of
> > numbers which tell you where the ORFs are located in the sequence.
> >
> > I have looked through all the documentation and still can not find this
> > feature even though it seem like an extremely common task.
> >
> > Thanks for any help,
> >
> > Lynn
> >
> >
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>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
>
>
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