[Bioperl-l] clustal w gap penalties

[Michael Bradley]

Bioperlers,
 
The placement of gaps in a multiple sequence alignments is more accurate
when guided by a secondary structure. What is the correct way to pass
Clustal w a sequence containing secondary structure or gap penalty
masks? I have tried to do this with Bio::AlignIO.
 
my $str = Bio::Align::IO->new ('-file' =>
'file_with_!SS_or_!GM_mask.aln') 
my $aln = $str->next_aln();
 
The 'file_with_!SS_or_!GM_mask.aln' is the standard Clustal
representation of this information and looks like this:
 
CLUSTAL W (1.83) multiple sequence alignment
 
!SS_seq   aaaAAAAAAaaa.bbbBBBBBBbbb       (where a/A denote helix and
b/B denote strand)
seq            MyAminoAcidSequenceGoesHere
 
or
CLUSTAL W (1.83) multiple sequence alignment
 
!GM_seq  222444444222111222444444222
seq            MyAminoAcidSequenceGoesHere
 
I get the sequence but the mask appears to be lost at this step. Any
suggestions?
 
I have found some discussion on the mail list about using
Bio::Seq::Meta::Array to create the mask followed by modifying some
aspect of Bio::Tools::Run::Alignment::Clustalw to pass the mask to
clustal w. Has anyone charted the course on this yet?
 
Mike Bradley