[Bioperl-l] reading gff3?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu Mar 12 18:42:08 EDT 2009


What's the trick to reading the fasta attached to gff files?
Bio:FeatureIO and Bio::Tools::GFF both seem to ignore it (unless I'm doing it wrong)

What I'm trying to do is read in a gff3 file (with attached fasta) then get the sequence for the CDS features contained within.

Any ideas?

Thanx,

--Russell 


Russell Smithies 
Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 
Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 

Toitu te whenua, Toitu te tangata 
Sustain the land, Sustain the people 


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



More information about the Bioperl-l mailing list