onal Biology
Notes
- Note 1
Introduction, genetic mapping
- Note 2
RFLP, gel electrophoresis, physical mapping
- Note 3
Sequencing, gene finding, similarity search, global alignment
- Note 4
Overlap detection, local alignment, space efficient Needleman-Wunsch
- Note 5
Bounded dynamic programming, the 4 russians speedup, general gap penalty function
- Note 6
Affine gap penalty function, multiple sequence alignment
- Note 7
Database search and BLAST
- Note 8
Substitution matrices, PAM, BLOSUM
- Note 8.5
Phylogenetic trees, the perfect phylogeny problem (character compatibility)
Some papers: How to determine the compatibility of undirected character state trees, Estabrook and Meacham.
A characterization of rigic circuit graphs (the colored triangulation equivalence), Buneman.
- Note 9
CpG islands, Markov chains, hidden Markov models
- Note 10
Forward and backward evaluation, HMM training
- Note 11
Pairwise alignment with HMMs
- Note 12
Physical mapping by restriction maps
- Note 13
Physical mapping by hybridization (non-unique probes)
- Note 14
Physical mapping by hybridization (unique probes)
- Note 15
DNA sequencing, shortest common superstring
- Note 16
Genome rearragement, sorting signed permutations by reversals
- Note 17
Genome rearragement, sorting signed permutations by reversals (cont.)
- Note 18
Finding maximal matches
- Note 19
Chaining local alignments
- Note 20
RNA secondary structure
- Note 21
Protein folding and threading
Slides
Note 1
Note 2
Note 3
Note 4
Note 5
Note 6
Note 7
Note 8
Note 9
Note 10
Note 11
Note 12
Note 13
Note 14
Note 15
Note 16
Note 17
Note 18
Note 16
Note 17
Note 18
Note 19
Note 20
Note 21
Homework
Homework 1 Solution
Homework 2 Solution
Homework 3, hard copies handed in
Homework 4
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.