Bioperl: mutation matrix question

[Max Nanao]

Hi All,
	Sorry for posting a question that is not specifically related
to Bioperl -- I'm using Bioperl to implement a simple sequence
analysis program, and I have a quick question regarding mutation matrices:
Is there a sensible way to score gaps in a mutation matrix?  Are
there matrices that include gap scores ?  I have a feeling that
this score will be related to the gap opening/closing/extention
values specified, but does it make any sense whatsoever to score
Gap to Gap as the maximum matrix score and Gap to anything else as
"0"?  I'm not talking about identity matrices here or Dayhof, but
something like Blosum or Pam.  Does anyone know of a good review
(web or otherwise) of scoring matrices?




Also, I have a fix (which  I notified Georg Fuellen about) for the
Clustal parsing feature of Bio::UnivAln ... 


   # Overwrite with values from file
   if ((defined($file)) && ($file ne $_NOFILE_FLAG) && ($file ne '')) {
     $self->_file_read($file,$ffmt);
   }
 >>>>  $ffmt='fasta' if ($ffmt /clustal/i);
 
   # Overwrite with values from @_
   $self->_seqs($seqs);
   $self->id($id);
   $self->desc($desc);
   $self->names($names);
   $self->row_ids($row_ids);
   $self->col_ids($col_ids);
   $self->row_descs($row_descs);
   $self->col_descs($col_descs);
   $self->numbering($numbering);
 




Thanks in advance!

Max

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