[Bioperl-l] pSW question- hanging tails of alignments

[Jason Stajich]

that is actuall local alignment behavior - look into a global  
alignment like needleman-wunsch implemented in EMBOSS in the tool  
'needle'.


On Mar 1, 2006, at 10:19 AM, Jon Manning wrote:

> Hi all,
>
> I'm using the Bio::Tools::pSW module to align two very similar
> sequences. But one is a little longer at the start than the other.
> Rather than showing this, pSW simply trims it off and it's not present
> in the resulting Bio::SimpleAlign object- a sort of BLAST-like  
> behaviour
> I suppose, showing only aligned regions. But is there a parameter I  
> can
> pass to allow these regions to be kept? Or am I doing something wrong.
>
> Incidentally, the behavior is the same in dpAlign.
>
> Thanks,
>
> Jon Manning
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12