[Bioclusters] Help

[Bruce ONeel]

Hi,

You might find 

Algorithms on Strings, Trees and Sequences by 
Dan Gusfield, ISBN 0521585198 to be useful.

cheers

bruce

"Arun M" <arun_mah@mec.ac.in> wrote:
> 
> Hi
> 
> Does anyone know of any simple/basic implementation of the BLAST
> methods/algorithm? What I mean is, the actual BLAST source code (both NCBI
> BLAST and WU-BLAST) is big and difficult to understand and require the use
> of libraries (like NCBI and Gish). I am looking for some code which
> implements just the essential(basic) methods of BLAST. That is, a program
> which performs just the basic "local alignment" search that is done by
> BLAST. Just a program which performs the very basic searching that "blastn"
> or "blastp" can do  -  and no advanced features, improved features or extra
> features such as blastx, tblastn, PSI Blast, PHI Blast, etc...
> 
> Secondly and lastly,  if anyone knows of any documents explaining (in an
> understandable way!) the working of BLAST - such as the use of the matrices,
> dynamic programming, local alignment stuff, etc.. - or about the
> implementation details, would you kindly let me know.
> 
> Thanx.
> 
> Arun
> 
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