[Bioperl-l] Clustalw and sensitivity to changes in 'pairgap' parameter??

[duxroq]

Hi,

For a project I am doing I wanted to maximize the gap penalty for a pairwise
alignment of a leader and a consensus sequence.  I experimented with
changing the 'pairgap' parameter.  However, Clustalw generated the same
exact alignment file no matter what I changed 'pairgap' to!  Why would this
happen? (As a side question, does 'pairgap' refer to the gap opening penalty
for pairwise alignments?  And does clustalw.pm have a parameter that
controls gap penalties for multiple alignments or for gap extensions?  My
computer did not recognize 'fixedgap' or 'floatgap' and therefore I assumed
I could only use 'pairgap' to modify my results).

Here are the relevant pieces of code:

# I set 'pairgap' to 50 because I think the default is 10 and I was seeking
to maximize the gap penalty, although I do not know the upper limit for
'pairgap' 
@params = ('pairgap' => 50);
$factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $aln_lead_cons = $factory->align(\@lead_cons_seqs);

Thank you!

Alexandria
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