CSE 8354 - Computatonal Biology

Course Description FALL 2004

Projects

Lectures
- Lecture 1 Introduction, genetic mapping
- Lecture 2 RFLP, gel electrophoresis, physical mapping
- Lecture 3 Sequencing, gene finding, similarity search, global alignment
- Lecture 4 Overlap detection, local alignment, space efficient Needleman-Wunsch
- Lecture 5 Bounded dynamic programming, the 4 russians speedup, general gap penalty function
- Lecture 6 Affine gap penalty function, multiple sequence alignment
- Lecture 7 Database search
- Lecture 8 Substitution matrices, PAM, BLOSUM
- Lecture 9 CpG islands, Markov chains, hidden Markov models
- Lecture 10 Forward and backward evaluation, HMM training
- Lecture 11 Pairwise alignment with HMMs
- Lecture 12 Physical mapping by restriction maps
- Lecture 13 Physical mapping by hybridization (non-unique probes)
- Lecture 14 Physical mapping by hybridization (unique probes)
- Lecture 15 DNA sequencing, shortest common superstring
- Lecture 16 Genome rearragement, sorting signed permutations by reversals
- Lecture 17 Genome rearragement, sorting signed permutations by reversals (cont.)
- Lecture 18 Finding maximal matches
- Lecture 19 Chaining local alignments
- Lecture 20 RNA secondary structure
- Lecture 21 Protein folding and threading

Slides
- Lecture 1
- Lecture 2
- Lecture 3
- Lecture 4
- Lecture 5
- Lecture 6
- Lecture 7
- Lecture 8
- Lecture 9
- Lecture 10
- Lecture 11
- Lecture 12
- Lecture 13
- Lecture 14
- Lecture 15
- Lecture 16
- Lecture 17
- Lecture 18
- Lecture 19
- Lecture 20
- Lecture 21

References
Durbin R. et al., Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids, chapters: 2, 3, 4, 10, 11.
Setubal J., Meidanis J., Introduction to Computational Molecular Biology, chapters: 1, 3, 4, 7, 8.
Pavel P., Computational Molecular Biology: An algorithmic approach, chapters: 1, 2, 3, 5, 10.
Gusfield D., Algorithms on Strings, Trees, and Sequences: Computer science and computational biology, chapters: 5, 6, 7, 12, 13, 14.
Waterman M., Introduction to Computational Biology: Maps, sequences, and genomes, chapters: 3, 4.

Problem Sets

Problem Set 1 Problem Set 2 Problem Set 3 Problem Set 4 Problem Set 5 Problem Set 6 etc...