Course Materials for Bioinformatics I
2006 NAR Database Issue
2006 NAR Web Server Issue
2007 NAR Database Issue
2007 NAR Web Server Issue
2008 NAR Database Issue
2008 NAR Web Server Issue
2009 NAR Database Issue
2009 NAR Web Server Issue
2010 NAR Database Issue
2010 NAR Web Server Issue
List of bioinformatic webservers
- Introduction to Bioinformatics I
- Homework assignments
- Material for lectures from the Jones/Pevzner book.
- Notes for Chaper 4, Brute Force Motif Searching,
(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
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;
"Multiple Alignment (Ch 6)"
- Weight matrices and introduction to probabilitic models
- Optional readings
You might find it amusing to read the
story of how I got involved in bioinformatics, or
"10 Steps to Success in Bioinformatics".