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.

Lectures

• Lecture 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 Primer on Molecular Genetics.
• Lecture 2: Introduction to sequence alignment. Global alignments and linear-space optimization.
• Lecture 3: Extensions to global alignments (i.e., "no-cost" start and end gaps, linear gap penalty functions), local alignments.
• Lecture 4: Database searching and BLAST.
• Lecture 5: Database searching continued, and introduction to multiple sequence alignments.
• Lecture 6: Recombinant DNA Technology.
• Lecture 7: Introduction to DNA sequencing and the human genome project.
• Lecture 8: Fragment assembly.
• Lecture 9: Genetic Mapping
• Lecture 10: Physical Mapping.
• Lecture 11: Gene Recognition.
• Lecture 12: Chip Technology.
• Lecture 13: Introduction to protein structure. Protein motif recognition.
• Lecture 14: Protein motif recognition: profile methods and hidden Markov models.

• Lecture 15: Threading.
• Lecture 16: Energy minimization: molecular dynamics.
• Lecture 17: Distance geometry.
• Lecture 18: Lattice models for protein folding.
• Lecture 19: Virus shell assembly.
• Lecture 20: Genome Rearrangements.
• Lecture 21: Phylogeny
• Lecture 22: Phylogeny
• Lecture 23: RNA secondary structure prediction

Handouts

• Handout 1: Course Information.
• Handout 2: Syllabus.
• Handout 3: Procedure for scribing lectures.
• Handout 4: Problem Set 1.
• Handout 5: Problem Set 2.
• Handout 6: Problem Set 3.
• Handout 7: Problem Set 1 solutions.
• Handout 8: Problem Set 4.
• Handout 9: Problem Set 5.