5.3 Further Reading

The following papers describe BLAST algorithms in more detail:

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). "Basic local alignment search tool," Journal of Molecular Biology, 215:403-10.
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucleic Acids Research, 25:3389-3402.
Gish, Warren and David J. States (1993). "Identification of protein coding regions by database similarity search," Nature Genet., 3:266-72.

For the latest information on NCBI-BLAST and other helpful documents, see the official web site at http://ncbi.nlm.nih.gov/BLAST.

The WU-BLAST web site (http://blast.wustl.edu) has several useful documents on BLAST in general, and includes pages specifically for WU-BLAST users. One of its most interesting documents is a thorough manual for the classic, ungapped version of BLAST 1.4 (http://blast.wustl.edu/doc/blast1.pdf).