onal Biology
Tentative 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 and BLAST
- 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 16
Lecture 17
Lecture 18
Lecture 19
Lecture 20
Lecture 21
Projects
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.
Homework
Homework 1 Due 09/23/09 Solution
Homework 2 Due 10/14/09 Solution
Homework 3 Due 11/11/09 Solution
Homework 4