[Bioperl-l] Information content of alignment

martin s9904982 at sms.ed.ac.uk
Thu May 13 09:32:19 EDT 2004

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.




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

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