参考文献

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25:3389-3402, September 1997. Stephen F. Altschul. Amino acid substitution matrices from an information theoretic perspective. Journal of Molecular Biology, 219:555-565, 1991. D. Haussler, A. Krogh, I. S. Mian, and K. Sjölander. Protein modeling using hidden Markov models: Analysis of globins. In Proceedings of the Hawaii International Conference on System Sciences, volume 1, pages 792-802, Los Alamitos, CA, 1993. IEEE Computer Society Press. Steven Henikoff and Jorja G. Henikoff. Position-based sequence weights. Journal of Molecular Biology, 243(4):574-578, November 1994. Liisa Holm and Chris Sander. Mapping the protein universe. Science, 273(5275):595-603, Aug 2 1996. R. Karchin and R. Hughey. Weighting hidden Markov models for maximum discrimination. Bioinformatics, 14(9):772-782, 1998. A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology, 247:536-540, 1995. Information on SCOP is available at http://scop.mrc-lmb.cam.ac.uk/scop. J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. Journal of Molecular Biology, 284(4):1201-1210, 1998. J. Park, S. Teichmann, T. Hubbard, and C. Chothia. Intermediate sequences increase the detection of homology between sequences. Journal of Molecular Biology, 273:349-354, 1997. William Pearson. Comparison of methods for searching protein sequence databases. Protein Science, 4:1145-1160, 1995. C. Sander and R. Schneider. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics, 9(1):56-68, 1991. E.L.L Sonnhammer, S.R. Eddy, and R. Durbin. Pfam: A comprehensive database of protein families based on seed alignments. Proteins: Structure, Function, and Genetics, 28:405-420, 1997. Julie D. Thompson, Desmond G. Higgins, and Toby J. Gibson. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research, 22(22):4673-4680, 1994.