[Bioperl-l] Capturing Joined Sequence from two records

Jason Stajich jason at bioperl.org
Mon Oct 15 18:54:38 EDT 2007


pass in a db handle to spliced_seq. There was a question about this  
on the list a few days ago.
http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html

  - does anyone want to add this solution in more example to FAQ?

-jason

On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:

> I have encountered a case of a protein sequence record for which the
> coding sequence is a join with ranges from two nucleotide sequence
> records:
>
> gi # is 7648673
>
> Relevant annotation is:
>
>    CDS             1..630
>                       /gene="KCND2"
>                       /coded_by="join
> (AF166007.1:430..1544,AF166008.1:345..507,
>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>                        
> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>
>
> Is there any way using Bio::Seq objects to seamlessly get the CDS
> nucleic acid sequence, or do I need to just treat it as an oddity and
> cobble together something manually?
>
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org

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