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