[Bioperl-l] ORF FInder

[Jason Stajich]

On Fri, 15 Feb 2002, Brian Osborne wrote:

> Lynn,
>
> You must be referring to the Docs Web page, and you're right,
> Bio::Factory::EMBOSS is not mentioned there since those pages only go as far
> as version 0.7.2. My guess is that this page is not created automatically,
> so it's not up-to-date. For more current documentation see
> http://doc.bioperl.org/bioperl-live/ but it looks like these pages aren't
> absolutely current either, but they're close and Bio::Factory::EMBOSS is
> mentioned (I don't see the Bio/Biblio directory, for example).
>
Hmm - my cronjob must not be working - will take a look.

> For the most recent code you might want to get a CVS account and download
> bioperl-live. I can't vouch for every single thing in bioperl-live but the
> code I've used works. Plus you'll be able to contribute!
>
NB - You don't have to have an account to checkout the code - see
http://cvs.open-bio.org for ways to browse the code online and to check
out anonymously.

> Brian O.
>
> ----- Original Message -----
> From: "Lynn Stevens" <lynn_m_stevens@hotmail.com>
> To: <b_i_osborne@hotmail.com>
> Sent: Thursday, February 14, 2002 8:04 PM
> Subject: Re: [Bioperl-l] ORF FInder
>
>
> >
> > Hi Brian,
> > I don't see Bio::Factory::EMBOSS on the BioPerl documents page.  Is this
> new?
> >
> >
> > >From: "Brian Osborne" <b_i_osborne@hotmail.com>
> > >To: "Lynn Stevens" <lynn_m_stevens@hotmail.com>
> > >CC: <bioperl-l@bioperl.org>
> > >Subject: Re: [Bioperl-l] ORF FInder
> > >Date: Thu, 14 Feb 2002 16:16:14 -0500
> > >
> > >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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> >
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu