Other useful resources

The BLAST web page hosted at NCBI
http://www.ncbi.nlm.nih.gov/BLAST

Download pages for the BLAST programs
http://www.ncbi.nlm.nih.gov/BLAST/download.shtml

Download pages for pre-formatted BLAST databases
ftp://ftp.ncbi.nlm.nih.gov/blast/db/

O'Reilly book on BLAST
http://www.oreilly.com/catalog/blast/

Explanation of scoring/substitution matrices and more
http://www.clcbio.com/be/