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

Michael Bradley mebradley at chem.ufl.edu
Mon Jun 14 12:30:10 EDT 2004

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); 
$seq = is a swiss-prot sequence with structural features recognizable by
Can anyone help me in obtaining $seq?
Mike Bradley

More information about the Bioperl-l mailing list