[Bioperl-l] Retrieve mRNA from Genome

Kevin Brown Kevin.M.Brown at asu.edu
Mon Apr 9 12:19:19 EDT 2007


I believe that is what the spliced_seq method is for

$feat->spliced_seq    # the "joined" sequence, when there are
                      # multiple sub-locations

http://www.bioperl.org/wiki/Bptutorial.pl 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Staffa, Nick (NIH/NIEHS)
> Sent: Monday, April 09, 2007 8:43 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Retrieve mRNA from Genome
> 
> I have been retrieving sub-sequence from Genbank genomic 
> records by use of Bio::SeqIO and ->get_SeqFeatures, ->start 
> ->end , but now I'm looking for a quick way to extract CDS or 
> mRNA from a multi-segmented annotation, e.g.
>      mRNA          
> join(72458..72791,84573..84613,93279..94419,94481..94656,
>                      
> 94719..94992,95056..95350,95438..95553,95614..96056)
> 
> Is there such a method?
> Please point me to appropriate documentation.



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