[Bioperl-l] Information content of alignment

[martin]

Hi Malay,

Not quite sure what you mean by 'information content'.  You can access a
single column of an alignment using the slice() function:

$aln2 = $aln->slice(20, 30)

which returns another AlignI object.  So something like;

foreach (0..$aln->length){
	my $column=$aln->slice($_, $_);
	# $column is now an AlignI object
	# do something with it....
}

you can get the documentation with 

% perldoc Bio::Align::AlignI

If you let me know what you want to do with the column, maybe I can give
some more advice.

Cheers

Martin

	

On Wed, 2004-05-12 at 18:56, Malay wrote:
> Hi Bioperlers:
> 
> Perdon my ignorance. I could not remove by haze about the numerous 
> bioperl modules. I looked as AlignI interface but could not gather the 
> answer to my question:
> 
> Is there any way to quickly calculate information content of each column 
> of the alignment in bioperl?
> 
> Any pointers or source code would be appreciated. Otherwise, I have to 
> get my hand dirty.
> 
> Cheers,
> 
> Malay
> 
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-- 
Martin Jones
The Nematode Genomics Lab
Institute of Cell, Animal and Population Biology
University of Edinburgh
King's Buildings
West Mains Road
Edinburgh, EH9 3JT