BLAST - How does BLAST work (Mar/26/2010 )
I would like to know how exactly the BLAST program works. Including the scoring matrix used, statistics. I am basically a molecular biologist and i am not familiar with math, statistics or computer science. Is there any source on how BLAST works that will be more understandable for a biologist?
have you looked at the blast page?
Or, perhaps even better, the BLAST chapter of the NCBI Handbook, or the BLAST Help Manual, or perhaps the article The Statistics of Sequence Similarity Scores?
Or, if you're just looking for the default setting for the various BLAST programs, you can find them here.