Cpt S 471/571: LECTURE NOTES
Introduction to computational biology and bioinformatics PDF PPT
Scribes: Intro 1 (by Matt Ferran)
Intro 2 (by Anwesha)
Sequence alignments
- Dynamic programming and alignment models:
Alignment introduction and global alignment PDF
(example alignment PPT)
Scribes: Sequence Alignment - Dynamic Programming algorithm (by Alireza Ghods)
Local alignment PDF
Scribes: Smith Waterman algorithm part 1 (by Wilson Garrett) Instructor scribes: Intro Algorithm
Affine gap
penalty PDF
Scribes: Intro to affine gap functions (by Biresh) Instructor scribe
Semi-global PDF
Scribe:
- Space-optimal global alignment PDF
Scribe:
- K-band
algorithm PDF
- Edit distance, other distance measures PDF
Scribe:
- Additional reading: Handbook of computational
molecular biology - Chapter 1
Exact Matching
- Introduction to look-up tables and BLAST
PPT PDF
Scribe:
-
Look-up table construction and introduction to TRIES (tries, compacted
tries and PATRICIA trees)
PDF
Scribe:
- Suffix trees PDF
Scribe:
- Suffix tree basic applications: Pattern
matching, longest common substring PDF
Scribe:
- Linear time construction algorithm (McCreight's
algo) PDF
Detailed algorithmic pseudocode: PDF
Here
is an example for simulating McCreight algorithm
PPT PDF
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- Bender-Farach algorithm for finding the Longest Common Ancestor (LCA)
in a suffix tree PDF
Scribe:
- Suffix tree advanced applications: approximate matching, restriction enzyme site, RNAi elements, suffix-prefix matching, maximal matching PDF
- Suffix array and LCP array, space
efficiency PDF
Scribe:
- Burrows Wheeler Transform (BWT) PDF
- Additional reading: Handbook of computational molecular biology - Chapters 5, 6
Probabilistic modeling for biological sequence analysis
- Probabilistic modeling PDF
- Markov chains and Hidden Markov Models PDF
- Viterbi decoding, Forward and Backward algorithms, and their use-cases PDF
- HMM-based sequence alignment PDF
- Additional reading: Durbin et al. - Chapters 1-4
Proteomics PDF
Genome scale problems
- Additional reading: Handbook of computational molecular biology - Chapters 8,9, 13
Phylogenetics
- Additional reading: Gusfield - Chapter 17
GENERAL READING AND REFERENCES
- Here is a good position paper by Sean Eddy about the general direction of computational biology & bioinformatics.
- A list of course-relevant journals in the area of bioinformatics and computational biology:
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Journal of Computational Biology