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

Daniel Jeffares dcj at sanger.ac.uk
Wed Mar 2 08:27:55 EST 2005

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 

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

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