18.417: Introduction to Computational Molecular Biology
This course gives an introduction to the basic computational methods
used for problems arising in molecular biology. We will focus on sequence
analysis, genomics, and protein folding. Topics include computational approaches
to: sequence homology and alignment, sequencing, physical and genetic mapping,
gene recognition, protein structure prediction, distance geometry, virus
shell assembly, and phylogeny.
Instructors: Bonnie Berger and Mona Singh.
Time and Place:Tuesdays and Thursdays, 1-2:30pm, 26-302.
Prerequisites: 6.001 or 18.410J/6.046J or permission of instructor.
No biology background is assumed.
1: A very basic introduction to molecular biology. A nice introduction
to this material and to genomics can be found in the Department of Energy's
on Molecular Genetics.
2: Introduction to sequence alignment. Global alignments and linear-space
3: Extensions to global alignments (i.e., "no-cost" start
and end gaps, linear gap penalty functions), local alignments.
4: Database searching and BLAST.
5: Database searching continued, and introduction to multiple sequence
6: Recombinant DNA Technology.
7: Introduction to DNA sequencing and the human genome project.
8: Fragment assembly.
9: Genetic Mapping
10: Physical Mapping.
11: Gene Recognition.
12: Chip Technology.
13: Introduction to protein structure. Protein motif recognition.
14: Protein motif recognition: profile methods and hidden Markov models.
16: Energy minimization: molecular dynamics.
17: Distance geometry.
18: Lattice models for protein folding.
- Lecture 19: Virus shell assembly.
- Lecture 20: Genome Rearrangements.
- Lecture 23: RNA secondary structure prediction
Bonnie Berger (firstname.lastname@example.org)
Mona Singh (email@example.com)