Algorithms for Molecular Biology: 1994 and 1995 Course Archive

Ron Shamir

This archive contains material of the course "Algorithms for Molecular Biology", taught by Ron Shamir (in Fall 94 and Fall 95 together with Dalit Naor , in the School of Computer Science at Tel Aviv University. This was a one-semester graduate course with one three-hour meeting each week.

Material available:

• Detailed course outline:
• Fall 95
• Fall 94
• Scribes of Fall 95 lectures:
• Lecture 1 biological background
• Lecture 2 inexact matching: edit distance
• Lecture 3 biological databases; the BLAST and FASTA algorithms (scribe missing)
• Lecture 4 RNA folding, evolutionary trees with binary and unrestricted characters
• Lecture 5 phylogenetic trees
• Lecture 6 phylogenetic trees - cont.
• Lecture 7 multiple sequence alignment
• Lecture 8 multiple sequence alignment - cont.
• Lecture 9 physical mapping models: consecutive ones matrices, interval graphs
• Lecture 10 physical mapping: recognition of interval graphs, interval sandwich problems, probabilistic models
• Lecture 11 physical mapping: most likely interval graph, chimeric clones, heuristic solutions
• Lecture 12 genome rearrangement, restriction maps.
• References for each topic
• general books on (computational and non-computational) molecular biology
• exact string matching (Fall 94 only)
• phylogeny (evolutionary trees)
• inexact string matching and RNA folding
• fast database searches
• multiple sequence alignment (Fall 95)
• multiple sequence alignment (Fall 94)
• shortest common superstring
• physical mapping
• genome rearrangement and restriction mapping
• Theoretical assignments, Fall 95
1. repeats, exact searches and searches with mismatches
2. phylogenetic trees
3. multiple sequence alignment, HMM and physical maps
• Hands-on assignments, Fall 95
1. evolutionary trees: formalizing a problem and using the Phylip package
2. exploring bioinformatic sites on the Internet: database searches, sequence comparison, viewing a structure
• Assignments, Fall 94
1. exact string matching and phylogeny
2. phylogeny, inexact matching
3. alignments, shortest common superstring
4. restriction and physical maps
• summary of replies to a request for course material which we posted on the network prior to the course
• updates: Additional information (in mail messages format) which we received after the initial posting of this page.

© Ron Shamir

Please send all feedback and comments to: rshamir@tau.ac.il

Last update: August 20, 1999