Course Materials for Bioinformatics I
Fall 2008

Lecture materials:

1. Introduction to Bioinformatics I
   • What is Bioinformatics I?
   • Basic Definitions
2. Basic Internet resources for bioinformatics
   • Homework assignment due Sept. 2
   • Homework assignment due Sept. 9
3. Basics of bioinformatic algorithms
   • Notes for Chaper 4 of the Jones/Pevzer book
   • Website for class notes from the Jones/Pevzner book Follow links Powerpoint Slides -> Chapter 5
   • 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 -> Chapter 8 (Graphs and DNA Sequencing)
4. Sequence alignment
   • Website -> Chapter 6
   • Notes about the dynamic-programming algorithm for aligning two sequences
   • Notes about alignments scores and Psi Blast
   • Linear-space alignment in revised notes
   • Website -> Chapter 7
   • Blast outline and paper
   • Multiple sequence alignment survey paper; recent paper about Clustal; website -> "Multiple Alignment (Ch 6)"
5. Weight matrices and introduction to probabilitic models
   • Notes on weight matrices (including an example about sorting by reversals)
   • Notes on probabilistic sequence models
   • Survey by Gary Stormo
   • Notes on log-odds methods
   • Amino-acid substitution scores
6. Hidden Markov Models
   • Notes
   • GenScan paper (see especially Figure 3)
   • Website -> Chapter 11 (HMMs)
7. Study guide.

Symposium on the Frontiers of Evolutionary Biology, Friday Oct. 10 at PSU.

Papers:

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