[Bioperl-l] Bio::LiveSeq::Transcript query from new bioperl user

[Heikki Lehvaslaiho]

Daniel,

While LiveSeq can be used for this, there is quite a lot of overhead in 
creating those objects. If you are going to apply this in a highthroughput
pipeline, I recommend you retrieve the CDS feature from the standard 
SeqIO-produced sequence object and determine the frame yourself.

Let me know in more detail what you want to do and I'll help you.

	-Heikki

On Wednesday 02 March 2005 13:27, Daniel Jeffares wrote:
> This is a request for help from a *very* new bioperl user. IM also
> pretty new to perl....
>
> I want to use the Bio::LiveSeq::Transcript->new method to make a
> transcript object from an .embl file.
>
> I then want to use the $frame = $transcript->frame($label) method so
> that I can trim sub-sections of the transcript to include only complete
> codons.
>
> So, in other words, I want to collect subsets of a transcript
> (coordinates that I have defined earlier), and then trim those
> coordinates to the nearest complete codons. And the get the sequence of
> those coordinates.
>
> ____________________________
> Daniel Jeffares
> Wellcome Trust Sanger Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SA, UK
> Phone: +44(0)1223 834244 x 7297
> ____________________________

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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