[Bioperl-l] Capturing Joined Sequence from two records

Warren Gallin wgallin at ualberta.ca
Mon Oct 15 18:25:14 EDT 2007


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


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