CSCE 471/871 (Spring 2013) lecture slides

• Lectures 0 and 1: Administrivia and Introduction, Jan 12–19, Chapter 1 (pdf6up)
  Also see:
• "Molecular Biology for Computer Scientists by Lawrence Hunter." In Artificial Intelligence and Molecular Biology, edited by Lawrence Hunter. ISBN 0-262-58115-9.
• The Cartoon Guide to Genetics, by Larry Gonick and Mark Wheelis. Harper Perennial, 1991, ISBN 0-06-273099-1.
• A Primer of Genome Science, by Greg Gibson and Spencer V. Muse. Sinauer Associates, Inc., 2005. ISBN 0-87893-232-1.
• Essential Cell Biology: An Introduction to the Molecular Biology of the Cell, by Bruce Alberts, Dennis Bray, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Garland Publishing, Inc., 1998. ISBN 0-8153-2045-0.
• Chapter 1 of Introuction to Computational Molecular Biology, by João Carlos Setubal and João Meidanis PWS Publishing Company, 1997. ISBN 0-534-95262-3.


• Lecture 2: Pairwise Alignments, Jan 19–Feb 2, Chapter 2 (pdf6up)
  Also see:
• The dynamic programming chapter of Introduction to Algorithms, Third Edition, by Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, and Clifford Stein. MIT Press and McGraw-Hill, 2010.
• Altschul, S.F. Amino acid substitution matrices from an information theoretic perspective. Journal of Molecular Biology, 219(3):555–565, 1991.
• Vingron, M. and Waterman, M.S. Sequence alignment and penalty choice. Review of concepts, case studies and implications. Journal of Molecular Biology, 235(1):1–12, 1994.
• Karlin, S. and Altschul, S.F. Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes. Proceedings of the National Academy of Sciences of the United States of America, 87:2264–2268, 1990.
• Henikoff, S. and Henikoff, J. G. Amino Acid Substitution Matrices from Protein Blocks. Proceedings of the National Academy of Sciences of the United States of America, 89:10915–10919, 1992. (BLOSUM Matrices)
• BLAST at the National Center for Biotechnology Information (NCBI)
• Wikipedia's BLAST article
• Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. Basic local alignment search tool. Journal of Molecular Biology, 215(3):403–410, 1990.


• Lecture 3: Hidden Markov Models, Feb 4–12, Chapter 3 (pdf6up)
  Also see:
• Section 9.6 of Pattern Recognition by Sergios Theodoridis and Konstantinos Koutroumbas
• K. Sjölander, K. Karplus, M. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. Computer Applications in the Biosciences (CABIOS), 12(4):327–345, 1996.


• Lecture 4: Profile Hidden Markov Models, Feb 14–19, Chapter 5 (pdf6up)
  Also see:
• Brown, M., Hughey, R., Krogh, A., Mian, I. S., Sjölander, K., and Haussler, D. Using Dirichlet mixture priors to derive hidden Markov models for protein families. In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, pages 47–55, 1993.
• K. Sjölander, K. Karplus, M. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. Computer Applications in the Biosciences (CABIOS), Vol. 12, No. 4, Pages 327–345, 1996.
• SAM: Sequence Alignment and Modeling System


• Lecture 5: Building Phylogenetic Trees, Mar 5–14, Chapter 7 (pdf6up)
Also see:
• Jotun Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when phylogeny is given. Mol. Biol. Evol., 6(6):649-668, 1989.
• Jotun Hein. A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol., 6(6):669-684, 1989.


• Spring Break, Mar 19–21


• Lecture 6: Multiple Sequence Alignments, Mar 26–Apr 9, Chapter 6 (pdf6up)
  Also see:
• SAM: Sequence Alignment and Modeling System
• MSA:
  • Humberto Carrillo and David Lipman. The multiple sequence alignment problem in biology. SIAM Journal on Applied Mathematics, Vol. 48, No. 5. (Oct., 1988), pp. 1073–1082. (MSA algorithm)
  • David J. Lipman, Stephen F. Altschul, and John D. Kececioglu. A tool for multiple sequence alignment. Proceedings of the National Academy of Sciences of the United States of America, Vol. 86, No. 12. (Jun. 15, 1989), pp. 4412–4415.
• Walter M. Fitch and Emanuel Margoliash. Construction of phylogenetic trees. Science, Vol. 155, No. 3760. (Jan. 20, 1967), pp. 279–284. (clustering in Feng-Doolittle)
• D. Feng and R. Doolittle. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution, Vol. 25, pp. 351–360.
• CLUSTALW:
  • CLUSTALW multiple sequence alignment program
  • Naruya Saitou and Masatoshi Nei. The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4:406-425, 1987. (used by CLUSTALW to build guide tree)
• Iterative refinement:
  • G. Barton and M. Sternberg. A strategy for the rapid multiple alignment of protein sequences. Journal of Molecular Biology, 198:327-337, 1987.
  • M. Berger and P. Munson. A novel randomized iterative strategy for aligning multiple protein sequences. Computer Applications in the Biosciences, 7:479-484, 1991.
  • O. Gotoh. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Computer Applications in the Biosciences, 9:361-370, 1993.

Last modified 09 April 2013; please report problems to sscott.