References

BLAST Introduction

Schuler, G.D. Sequence alignment and database searching. Methods Biochem Anal. 2001;43:187-214. (PubMed)
(This is also chapter 8 of Baxevanis, A.D. and Ouellette, B.F.F. Bioinformatics: A practical guide to the analysis of genes and proteins, 2nd ed. John Wiley and Sons. New York, NY.)

BLAST Help Documentation

Accessible from the BLAST home page. FAQs are also accessible from the BLAST WWW page.

Additional articles:

See articles cited on the various BLAST web site. Some of those articles are also cited on the search results pages.
Ye J, McGinnis S, Madden TL. BLAST: improvements for better sequence analysis. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W6-9. (PubMed; full text)
Pertsemlidis A, Fondon JW 3rd. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2001;2(10):REVIEWS2002. Epub 2001 Sep 27. (PubMed)
Additional articles are cited on the references slide of the Similarity Searching module of the NCBI Advanced Workshop for Bioinformatics Information Specialists

BLAST		Revised 11/05/2007