[Bioperl-l] calculate the frequency of occurrence of the mostcommonly observed amino acid at each position of multiplesequence alignment

Mark A. Jensen maj at fortinbras.us
Sat Feb 7 11:25:43 EST 2009


Dylan,

This is an extremely good exercise for anyone learning Perl to do 
bioinformatics.
When you have done many exercises like this, you will see what people mean
when they say it is very straightforward.

Here are some hints:

Use the "entropy" scrap at 
http://www.bioperl.org/wiki/Site_entropy_in_an_alignment .
You will convert the function entropy_by_column() into the function you need.
Replace the line

 $ent{$col} = entropy(values %res);

with a line you will write using the "hash key at max value" scrap, found
here: http://www.bioperl.org/wiki/Hash_key_at_the_max_value .

Happy coding!
Mark

----- Original Message ----- 
From: "Dylan Krishnan" <dylankrishnan at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Saturday, February 07, 2009 11:10 AM
Subject: [Bioperl-l] calculate the frequency of occurrence of the mostcommonly 
observed amino acid at each position of multiplesequence alignment


>I am new to perl but this is somethign I am seeking to do either through a
> bioperl module or just perl. Apparently, this is quite "straightforward
> using PERL," but I beg to differ.
>
> Any assistance regarding this matter would be greatly appreciated.
>
> Thanks!
>
> -dylan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> 



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