Lecture 13 Nov 2001, Per Kraulis

Hidden Markov models

1. Regular expressions
2. PROSITE patterns and rules
3. Sensitivity and specificity
4. Sequence profiles
5. Hidden Markov models
6. Pfam and HMMER
7. PSI-BLAST

Chapters in the course book ("Introduction to bioinformatics", T K Attwood and D J Parry-Smith):

• Chapter 7, "Multiple sequence alignment"
• Chapter 8, "Secondary database searching"