Bioperl: mutation matrix question

[Ewan Birney]

On Thu, 4 May 2000, Max Nanao wrote:

> 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?
> 

Read the probabilistic modelling book Durbin, Eddy Krogh and Mitchinson.

Probabilistic models gives you a principled ways of setting 'scores'
for gaps and all manner of other things.


> 
> 
> 
> 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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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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