Texts
The required textbook for this course is
- Biological Sequence Analysis: Probabilistic Models
of Proteins and Nucleic Acids, R. Durbin et al.
Cambridge University Press, 1998.
For additional biological background,
- The Cartoon Guide to Genetics by Larry Gonick and Mark Wheelis.
is recommended.
In addition, there are two recommended texts:
- Introduction to Computational Molecular Biology, J.C.
Setubal and J. Meidanis
- Bioinformatics: Sequence and Genome Analysis,
D.W. Mount.
These books will be on reserve in both the Mellon and Engineering libraries.
Additional reading materials 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.
Readings by topic
| 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, 64-66, 89-98; (electronic reserve)
Durbin, pp. 17-24, 29-30 (course text)
Saving space, Setubal and Meidanis, 58-60; (physical reserve)
General gap penalty functions, Setubal and Meidanis, 60-64 (physical reserve)
|
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| 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 (course text)
|
On the Design of Optimization Criteria for MSA, Durand and Farach-Colton, In Biological Evolution and Statistical Physics, M. Laessig and A. Valleriani, Eds,Springer Verlag, 2002
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: (course text)
- 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
|
Parsimony, nice examples
Mount, pp 248-254(physical reserve)
Computing rate corrected distances:
Phylogeny notes, pp. 13-17
Durbin et al, 8.2 (course text)
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) |
Hidden Markov Models
Local multiple sequence alignment
|
Ewens & Grant, pp 327-340 (electronic reserve)
Durbin et al, 3.1 - 3.4 (course text) |
Mount, pp 161-198 (physical reserve) |
| 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 (course text)
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 (course text)
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 |
|
| Gene finding |
Mount, pp 338 - 351 (electronic reserve)
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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