References

Reeck et al. Cell 50(5): 667 (1987) (see "Homology" slide) Marchler-Bauer et al. Nucleic Acids Res 30(1):281-3, 2002. (see slides on BLink; CDD) Needleman, S.B. and Wunsch, C.D. J Mol Biol. 48(3):443-53 (1970). (see "Why BLAST?" slides) Smith, T.F. and Waterman, M.S. J Mol Biol. 147(1):195-7 (1981). (see "Why BLAST?" slides) Pearson, W.R. and Lipman, D.J. Proc Natl Acad Sci U S A. 85(8):2444-8 (1988). (see "Why BLAST?" slides) Altschul et al. Nucleic Acids Res. 25(17):3389-402 (1997). (see "Why BLAST?" slides) Altschul et al. J. Mol. Biol. 215(3):403-10, 1990. (see "Why BLAST?" slides) McLysaght, A. Molecular Evolution Lab Tutorials and Guides (July 16,2004) (see "Why BLAST?" slides) Pearson, W.R. Protein sequence comparison and Protein evolution Tutorial - ISMB2000 (October, 2001) (June 15, 2004) (see "FASTA" slides) Henikoff and Henikoff. Proc Natl Acad Sci U S A 89(22):10915-9, 1992. (PAM and BLOSUM) Dayhoff, Schwartz, and Orcutt Atlas Protein Seq. Struc. 5:345–352, 1978 (PAM and BLOSUM derivation) Altschul, S.F. J Mol Evol 36:290-300, 1993. (see clides on "multiple searches") Wakely, Mol Biol Evol 11(3):436-42, 1994. (see slides on "Transversion vs. Transition") States et al. Methods 3(1):66-70, 1991. (see slides on "Transversion vs. Transition") Pagni, M. and C. V. Jongeneel. Briefings in Bioinformatics 2(1):51-67, 2001. (see "BLAST statistics" slides) Schaffer, AA. et al. Nucleic Acids Res. 2001 29(14):2994-3005. (Compositional adjustment) Yu YK, Wootton JC and Altschul, SF. Proc Natl Acad Sci U S A. 2003 100(26):15688-93. (Compositional adjustment) Yu, YK and Altschul, SF. Bioinformatics. 2005 21(7):902-11. (Compositional adjustment) Wootten, J.C. and Federhen, S. Methods in Enzymology 266:554-71, 1996. (BLAST filters) Geer et al. Genome Res. 12(10):1619-1623, 2002 (RPS BLAST) Additional References: A good source of references about BLAST and other bioinformatics resources is the BLASTinfo page from NCBI. Korf, I., Yandell, M., and Bedell, J. (2003). Blast. O'Reilly, Beijing ; Farnham.