[Bioperl-l] A question about Bioperl SeqUtil

[Smithies, Russell]

How about running your chromosomes through getorf or similar from EMBOSS then translating just the ORFs (with 6-frame or BioPerl)?

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hui Liu
> Sent: Tuesday, 14 June 2011 2:10 a.m.
> To: Chris Fields
> Cc: BioPerl List
> Subject: Re: [Bioperl-l] A question about Bioperl SeqUtil
> 
> Hi Chris,
>     Sorry. I will send to bioperl List next time. So my current problem
> is
> that large sequence will 'out of memory'  using Bio::SeqUtil. It is of
> 500Mb
> size. Anyway, I will try to do something in my Perl code to divide the
> sequences.
>      Thanks :-)
> Hui
> On Sat, Jun 11, 2011 at 6:26 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> 
> > Hui,
> >
> > Please email questions to the mail list, not directly to individual
> > developers.
> >
> > You probably could translate whole chromosomes this way, but it might
> take
> > a while.  I would also look at tools like EMBOSS to do this, should
> be
> > faster.
> >
> > chris
> >
> > On Jun 11, 2011, at 10:31 AM, Hui Liu wrote:
> >
> > > Hi Chris,
> > >      Now I am having trouble translating large chromosome sequences
> in 6
> > frames. Do you know any available tools that supports large sequence
> > translation? Does Bioperl 1.6.90 support that?
> > >      Thanks a lot :-)
> > > Hui
> > > --
> > > Nothing shocks me. I'm a scientist.
> > >                              -Indiana Jones
> >
> >
> 
> 
> --
> Nothing shocks me. I'm a scientist.
>                              -Indiana Jones
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