[Bioperl-l] BLOSUM matrix

[Chris Fields]

Hmm, beginner programmer, wants to learn perl?  Here are some  
directions:

http://learn.perl.org/

Start with Schwartz's latest incarnation of Learning Perl, then work  
your way up to Intermediate Perl (I think Mastering Perl is on the  
horizon...)

For some pointers using Perl and bioinformatics, pick up Tisdall's  
books Beginning/Mastering Perl for Bioinformatics.

This is really a list for bioperl, not perl and bioinformatics  
(thought the two cross here all the time!).  We normally don't mind  
answering questions but we typically don't do people's homework  
unless we're unusually bored.  And we can be excessively cranky when  
someone repeatedly posts requests for something that shouldn't take  
much reading and Googling to find out.  Again, we're not into that  
homework gig, i.e. 'walking you through it' is tantamount to 'doing  
it for you.'

1)  Arrays and how to use them are in Learning Perl; there are  
probably better ways to do this than an array, though...
2)  Use Torsten's link to get you started.

Chris

On Jul 16, 2006, at 9:33 PM, Sudha Gunturu wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign