[Bioperl-l] Capturing Joined Sequence from two records

Chris Fields cjfields at uiuc.edu
Mon Oct 15 21:39:37 EDT 2007


Would spliced_seq() work with a protein sequence this way?  The  
location string is in a tag 'coded_by', which would require a little  
more work to get the sequence.

chris

On Oct 15, 2007, at 5:54 PM, Jason Stajich wrote:

> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list