03511 - Readings

Computational Molecular Biology and Genomics - Assigned Readings


There is no required textbook. No single textbook covers all of the material covered in the course. Reading materials drawn from several textbooks, as well as the primary literature, will be available through the library's electronic reserve system and links from this page. Electronic materials are available on the cmu.edu subnet only.

The Cartoon Guide to Genetics, by Larry Gonick  and Mark Wheelis, is recommended for those needing additional biological background. It is available in the campus bookstore.

For supplementary reading, the following textbooks are recommended:

These books will be on reserve in both the Mellon and Hunt libraries. PDF copies of the relevant material are linked below.

Readings by topic

For those who wish to read the material before class, reading assignments are listed below. Topics will not necessarily be covered in the order given.

Pairwise sequence comparison
  • Setubal and Meidanis, 47-57, 89-92, 96-98; (electronic reserve)
  • Durbin, 17-24 (electronic reserves)
  • Saving space, Setubal and Meidanis, 58-60; (physical reserve)
  • General and affine gap penalty functions,
    - Setubal and Meidanis, 60-66 (physical reserve)
    - Durbin, 29-30 (electronic reserves)
  • Substitution models
  • Background: Markov chains
  • Models of nucleotide substitution
  • Markov Chain background
    - Ewens and Grant, 4.4-4.8 (electronic reserves), 6.1-6.4 (physical reserves)
    - Durbin et al., 48-51 (Section 3.1) (electronic reserves)
    Models of nucleotide substitution
    - Durbin et al., 8.2, pp. 193 - 197 only (electronic reserves)
    Amino acid substitution matrices
    Substitution matrices, PAM matrices:
    - Setubal and Meidanis, 80-84; (electronic reserve)
    - Mount, pp. 76-89; (electronic reserve)
    - Durbin et al, pp. 14-16 (electronic reserves)
    BLOSUM Matrices:
    - Ewens and Grant, 6.5.2. (electronic reserves)
    - Amino acid substitution matrices from protein blocks, Henikoff S, Henikoff JG., PNAS 89(22):10915-9, 1992 (electronic reserve)
    Position specific scoring matrices (PSSMs), the Gibbs sampler
    Gibbs sampler
    Ewens and Grant, 211-215. (electronic reserve).
    Theoretical framework, convergence proofs
    - Ewens and Grant, 10.5.2, (physical reserves).
    - Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Lawrence et al., Science. 1993 262(5131):208-14.
    - Explaining the Gibbs sampler, G. Casella & E. I. George, The American Statistician, 46:167-174, 1992
    Hidden Markov Models
  • Ewens & Grant, 327-340 (electronic reserves)
  • Durbin et al, 3.2 - 3.4 (electronic reserves)
  • Mount, pp 161-198 (physical reserve)
  • Pseudocounts:
  • - Durbin, et al 5.6 (electronic reserves)
    - Hidden Markov Models in Computational Biology: Applications to Protein Modeling,
    Krogh et al., JMB 235, pp 1501--1531,(1994).
    Available through electronic reserves.
    Applications of HMMs to molecular biology
  • Durbin et al, 5.1 - 5.4 and 149-154, 158 (electronic reserves)
  • Hidden Markov Models in Computational Biology, Krogh et al., JMB,235, 1501-1531, 1994 (electronic reserve)
    Database Searching
  • Mount, 282-291 (electronic reserve)

  • BLAST:
    - Setubal and Meidanis, 84-87 (electronic reserve)
    - Basic local alignment search tool, Altschul et al. , J. Mol. Bio., 1990 (electronic reserve)
    - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Altschul et al. ,Nucleic Acids Research, 1997, pp. 3389 - 3394 (electronic reserve)

    BLAST statistics:
    - The statistics of sequence similarity scores S. F. Altschul

    Using BLAST in practise:
    - Blast tutorial
    Blast statistics:
    - Amino acid substitution matrices from an information theoretic perspective S. F. Altschul, J. Mol. Bio., 219:555-565, 1991 (electronic reserve)
    - A protein alignment scoring system sensitive at all evolutionary distances, S. F. Altschul, J. Mol. Evol., 36:290-300 , 1993 (electronic reserve)
    - Statistical Methods in Bioinformatics, W. Ewens and G. Grant (Physical reserves)

    Other BLAST references
    Global multiple sequence alignment
  • Setubal and Meidanis, 69-72 (electronic reserve)
  • Durbin, 6.1 -- 6.4 (electronic reserves)
  • Protein multiple sequence alignment, Do and Katoh, 2008. (electronic reserves)
  • Strategies for multiple sequence alignment, Nicholas HB Jr, Ropelewski AJ, Deerfield DW 2nd, Biotechniques 2002 Mar;32(3):572-4 (electronic reserve)

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    Last modified: August 26, 2019.
    Maintained by Maureen Stolzer and Dannie Durand.