References
- For historic overview: Mount
book Chapter 1
- For basic probability and
statistical models: Durbin book Chapter 1.3 (page 4-11)
- For molecular biology:
course notes, your bio buff friends, Alberts's
Molecular Biology of the Cell
- For an extensive review of
probability: Ewens book Chapter 1.1--1.5, 1.8--1.10, Chapter 3.
- Durbin book: Chapter 2.1,
2.2
- Ewens book: Chapter 6.1--6.3
- Mount book: Chapter 3,
Introduction
- Durbin: Chapter 2.3,
Alignment algorithms
- Mount: Chapter 3, pp 59-76
- Ewens: Chapter 6.4
For scoring matrices
- Mount: Chapter 3, pp 76-90
- Ewens: Chapter 6.5
To teach yourself more complicated dynamic programming (optional)
- (Optional) Ewens: Chapter
9.2.5-7 (pp.275--279) on the math of scores and E-values
- Durbin: Chapter 2.7,
Significance of scores
- Mount: pp90--96, Scoring
matrices; pp96--103, Significance of scores; pp300--307, BLAST
- NCBI BLAST home, click on
"tutorial" on the left. Some
interesting topics.
- Durbin: Chapter 6.3, Multiple
dynamic programming
- Durbin: Chapter 3.3, HMM parameter estimation
- Durbin: Chapter 5.1-5.3, profile HMM for
Seventh Week
- Durbin: Chapter 8 (section 3 and 5 can be skipped)
Seventh Week
- Mount: Chapter 8, Gene
Prediction