[Bioperl-l] Count or weight matrix in bioperl?

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Feb 8 21:54:39 EST 2006


>   Say I have an array of nucleotide sequences of of length N.  I  want to calculate the count matrix (weight matrix). That is for each  position 1..N, I want to know how many As, Cs ,Ts and Gs there  are.  Is the code to do this already written in bioperl to build  this matrix if I pass it those strings?
>   Please excuse my lack of knowledge as I am a new comer to bioinformatics.

Use the Bio::Tools::SeqStats module. The PDoc documentation even has an 
example similar to what you want to do:

http://doc.bioperl.org/releases/bioperl-1.5.0-RC1/Bio/Tools/SeqStats.html

--Torsten Seemann



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