[Bioclusters] Help

Bruce ONeel bioclusters@bioinformatics.org
Mon, 24 Jun 2002 15:53:08 +0200


You might find 

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



"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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