[Bioperl-l] clustal alignments with structural based gap penalties

[Michael Bradley]

Hello,
 
I would like to be able to use the secondary structure assignments of a
swiss-prot sequence entry to set gap penalties when aligning a set of
homologous proteins with Clustal. 
 
For example, I am able to do steps 1 and 2: 
 
Step 1: $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
Step 2: $aln = $factory->align($seq_array_ref)
 
I would then like to do step 3:
 
$aln2 = $factory->profile_align($aln1,$seq); 
 
where,
$seq = is a swiss-prot sequence with structural features recognizable by
Clustal.
 
Can anyone help me in obtaining $seq?
 
Mike Bradley