[Bioclusters] Help

Arun M bioclusters@bioinformatics.org
Mon, 24 Jun 2002 16:34:26 -0530 (IST)


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.