COS 551 Computational Biology Lecture Notes

Princeton University
Computer Science Dept.

Lecture Notes for Computer Science 551
Introduction to Computational Molecular Biology and Genomics

Mona Singh

Sequence Comparison.

Global sequence alignment
Local sequence alignment
Multiple sequence alignments, part I, part II, slides
Substitution matrices--PAM and Blosum.
Database Searching: Blast and Fast. (Draft notes)

Sequence Motifs.

Motifs and profile analysis.
Motif finding using Gibbs Sampling and EM.
HMMs and profile analysis, 2000 draft notes

Phylogeny notes, slides . These Notes cover:

Distance based-methods
Calculating distances from sequence data
Parsimony
Maximum likelihood
Bootstrapping

Protein structure.

Protein structural motif recognition
Protein threading
Protein secondary structure prediction notes, Review article.
Protein-protein interactions

Gene Finding.

Gene expression analysis.

RNA secondary structure prediction.

Genome rearrangements.

Introductory Materials to molecular biology and the human genome project can be found in:

Hunter's molecular biology for computer scientists.
The Department of Energy's Primer on Molecular Genetics.
The Department of Energy's Overview of the Human Genome Project.

I also have course notes from a previous course I co-taught with Bonnie Berger (Spring 1998, 18.417 at MIT): Introduction to Computational Molecular Biology

These course notes developed in part with support from NSF Pecase Award MCB-0093399.