[Bioperl-l] BLOSUM matrix

[Sudha Gunturu]

Sorry for not being clear with my question.  Let me try to explain.  I want to Implement dynamic programing using Blosum as scoring matrix.
   
  1. I want to know how to define the values of Blosum in an array.
  2. What functions are suitable for global alignment of two sequences. Etc.,
   
  Being a beginer programer want some direction, books, and good websites which can help me in achieving the implementation.  It would be great if someone can walk me through this.
   
  Thanks
  Sudha

Torsten Seemann <torsten.seemann at infotech.monash.edu.au> wrote:
  Sudha,

> Being a beginner perl programming, was wondering if anyone can help me with implementation of BLOSUM 65 matrix for the following alignments or in 
general. Any inputs, websites to help with this are appreciated.
> AILCAA
> ALLLAA
> ILIICL

The BLOSUM65 matrix does not define a method for alignment, it just 
provides some parameters. Perhaps you should read this first:

http://en.wikipedia.org/wiki/Sequence_alignment

-- 
Dr Torsten Seemann http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia



 		
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