[Bioperl-l] Alignment

Jay Hannah jay at jays.net
Tue Feb 20 19:27:01 EST 2007

> On 2/20/07, marian thieme <marian.thieme at lycos.de> wrote:
>> I have a series of sequences which should be aligned against a 
>> reference sequence.
>> In this special case we dont need to calculate anything, we only need 
>> to represent the sequences and get for instance some columns of 
>> interest.
>> The problem now is, that some sequences have gaps and we need to 
>> represent gaps in the rewference sequence as well as in some 
>> individual sequences.

On Feb 20, 2007, at 9:30 AM, Albert Vilella wrote:
> I think the SimpleAlign object contains a set of sequences, each of
> which is a LocatableSeq object.

Fascinating. In my BLAST-centric universe I went and rolled my own 
solution for SeqLab where I hold onto the Bio::Seq from the reference 
sequences and then hold onto the Bio::Search::HSP::GenericHSP objects 
for all my BLAST hits. From that dataset I can write whatever reports I 
want and/or perform any subsequent actions. I wonder if I should have 
done that differently...

What typically creates .pfam files?


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