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

Jon Manning jrm at compbio.dundee.ac.uk
Wed Mar 1 10:19:19 EST 2006

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.


Jon Manning

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