Identification of common molecular subsequences
Smith TF, Waterman MS
J Mol Biol 1981 Mar 25;147(1):195-7
Basic local alignment search tool
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.
J Mol Biol. 1990 Oct 5;215(3):403-10.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ
Nucleic Acids Res 1997 Sep 1;25(17):3389-402
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
Karlin S, Altschul SF
PNAS. 1990 Mar;87(6):2264-8.
Applications and statistics for multiple high-scoring segments in molecular sequences.
Karlin S, Altschul SF
PNAS 1993 Jun 15;90(12):5873-7.
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV and Altschul SF
Nucleic Acids Res.i 2001 29:2994-3005
The compositional adjustment of amino acid substitution matrices
Yu Y-K, Wootton JC and Altschul SF
PNAS 2003 100:15688-15693
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
Yu Y-K and Altschul SF
Bioinformatics 2005 21:902-911
Protein database searches using compositionally adjusted substitution matrices
Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schaffer AA and Yu Y-K
FEBS J 2005 272(20):5101-9
Improved tools for biological sequence comparison.
Pearson WR, Lipman DJ
PNAS 1988 Apr;85(8):2444-8
Flexible sequence similarity searching with the FASTA3
program package
Pearson, W. R.
Methods Mol. Biol. (2000) 132:185-219 pdf
This is a nice review of when to run which program.
BLAT -- The BLAST-Like Alignment Tool.
Kent WJ
Genome Research (2002) 4:656-664.