Computational Molecular Biology and Genomics Reading

Texts

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 Engineering libraries.

Readings by topic

For those who wish to read the material before class, reading assignments are listed below. Topics will be covered in the order given.
TOPIC
ASSIGNED READING
ADDITIONAL TOPICS
Pairwise sequence comparison
  • Global sequence alignment notes,
  • Local sequence alignment notes,
      courtesy Dr. M. Singh, Princeton University
  • Setubal and Meidanis, 47-52, 55-57, 89-98; (electronic reserve)
  • Durbin, pp. 17-24, 29-30 (electronic reserves)
    		•
  • Saving space, Setubal and Meidanis, 58-60; (physical reserve)
  • General and affine gap penalty functions, Setubal and Meidanis, 60-66 (physical reserve)
    • Global multiple sequence alignment
  • Setubal and Meidanis, 69-72 (electronic reserve)
  • Multiple sequence alignment notes, I,
  • Multiple sequence alignment notes, II,
      courtesy Dr. M. Singh, Princeton University
  • Durbin, 6.1 -- 6.4 (electronic reserves)
  • Protein multiple sequence alignment , Do and Katoh, 2008.
  • Strategies for multiple sequence alignment, Nicholas HB Jr, Ropelewski AJ, Deerfield DW 2nd, Biotechniques 2002 Mar;32(3):572-4 (electronic reserve)
    		•
    Phylogeny reconstruction
  • Phylogeny notes,
      courtesy Dr. M. Singh, Princeton University
    Durbin, et al: (electronic reserves)
    7.1, 7.2:  Background on trees
    7.4:  Parsimony
    7.3:  Distance-based methods
    pp. 197 - 207:  Maximum Likelihood
    7.5:  Assessing phylogenies with bootstrap resampling
    pp. 224 - 231:  Comparison of methods

    Felsenstein Inferring Phylo- genies, Chapter 11, Sinauer Associates, 2003.
    pp.161-169:  UPGMA and NJ
    		•  Parsimony, nice examples
  • Mount, pp 248-254(physical reserve)

    Computing rate corrected distances:
  • Phylogeny notes, pp. 13-17
  • Durbin et al, 8.2 (electronic reserves)

    Complexity results:
  • On the Approximability of Numerical Taxonomy: (Fitting Distances by Tree Metrics), Agarwala et al. , (SODA '96) (electronic reserve)
  • Efficient Algorithms for Inverting Evolution, Farach and Kannan, (STOC '96)

    In-depth treatment of phylogeny reconstruction:
    Felsenstein, Inferring Phylogenies, Sinauer Associates, 2003.
    • Hidden Markov Models
    Local multiple sequence alignment
  • Ewens & Grant, pp 327-340 (electronic reserve)
  • Durbin et al, 3.1 - 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
  • Profile Hidden Markov Models,
      courtesy Dr. M. Singh, Princeton University
  • Durbin et al, 5.1 - 5.4 and pp 149-154, 158 (electronic reserves)
  • Hidden Markov Models in Computational Biology, Krogh et al., JMB,235, 1501-1531, 1994 (electronic reserve)
    		•  
    Substitution matrices
  • Setubal and Meidanis, 80-84; (electronic reserve)
  • Mount, pp 76-89; (electronic reserve)
  • Durbin et al, pp 14-16 (electronic reserves)
  • Amino acid substitution matrices from protein blocks, Henikoff S, Henikoff JG., PNAS 89(22):10915-9, 1992 (electronic reserve)
    		•  
    Database Searching
  • Mount, pp. 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
    • Gene finding
    (Time permitting)
  • Mount, pp 338 - 351 (electronic reserve)
  • Defining genes in the genomics era.
    Snyder and Gerstein, Science (2003) 300(5617):258-60.
  • Yeast rises again.  S. Salzberg, Nature ( 2003) 423, 233-234
  • Gene Discovery in DNA Sequences
    S. Salzberg, IEEE 1999 (electronic reserve)
  • A hidden Markov model that finds genes in E. coli DNA A. Krogh et al., NAR 1994 (electronic reserve)
  • Prediction of Complete Gene Structures in Human Genomic DNA C. Burge and S. Karlin, JMB 1997 (electronic reserve)
    		•
  • Assessment of protein coding measures
    J.W. Fickett and C.S. Tung, NAR 1992 (electronic reserve)
  • Distinctive sequence features in protein coding genic non-coding, and intergenic human DNA R. Guigo and J.W. Fickett, JMB 1995 (electronic reserve)
  • Evaluation of Gene Structure Prediction Programs M. Burset and R. Guigo, Genomics 1996 (electronic reserve)


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    Last modified: August 22nd, 2010.
    Maintained by Dannie Durand (durand@cs.cmu.edu).