Course Materials for Bioinformatics I
Fall 2010

Lecture materials:

1. Introduction to Bioinformatics I
   • What is Bioinformatics I?
   • Basic Definitions
2. Homework assignments
   • Assignment due Aug. 30
   • Assignment due Sept. 2
   • Assignment due Sept. 13
3. Material for lectures from the Jones/Pevzner book.
   • Notes for Chaper 4, Brute Force Motif Searching, pdf. (A PowerPoint version can be found here.)
   • Notes for Chaper 5 of the Jones/Pevzer book. Read pp. 125-138.
   • In Jones/Pevzner read about:
     • NP-complete problems, pages 49-51
     • graphs, and the Eulerian and Hamiltonian Cycle Problems, pages 248-258
     • the Shortest Superstring Problem, pages 264-265
     • Sequencing by Hybridization, and two solutions, pages 268-275
     • Website for Chapter 8 (Graphs and DNA Sequencing)
   • Sequence alignment
     • The Change Problem: read pp. 17-24, 148-152.
     • The Manhatten Tourist Problem: read pp. 153-161.
     • Longest Paths in Directed Acyclic Graphs (DAGs): read pp. 162-166.
     • Website for introduction to dynamic programming.
     • Notes about the dynamic-programming algorithm for aligning two sequences
     • Notes about alignments scores and Psi Blast
     • Blast outline and paper
     • Multiple sequence alignment survey paper; recent paper about Clustal; website -> "Multiple Alignment (Ch 6)"
   • Weight matrices and introduction to probabilitic models
     • Notes on weight matrices.
     • Survey by Gary Stormo
     • Notes on log-odds methods
     • Notes on probabilistic sequence models
     • Amino-acid substitution scores
4. Optional readings
   • UCSC Browser
   • 28-way genome alignment
   • Blanchette et al. 2006
   • Galaxy
   • mapping tools, or here.

You might find it amusing to read the story of how I got involved in bioinformatics, or "10 Steps to Success in Bioinformatics".