Bioinformatics - Lent 2009

Supervisor: Hyoungshick Kim

Our goal is to learn and understand fundamental algorithms to analyze DNA and protein sequences.

We cover the following topics:

1. Sequence alignment (I): Needleman-Wunsch algorithm, Smith-Waterman algorithm, etc.

2. Sequence alignment (II): Four-Russian algorithm, BLAST, PatternHunter, etc.

3. Phylogenetic analysis: Sankoff algorithm, Fitch algorithm, UPGMA, neighbour joining, etc.

4. Hidden Markov Model

Policies

1. Scheduling
1. If you have a good reason to reschedule (illness, emergency, etc.), e-mail me and your co-supervisees as early as possible so that we can all discuss rescheduling.
2. Assigned work
1. Assigned work should be submitted by 1500h the day before the supervision.
2. Electronic submission of work is preferable. If you submit handwritten work, please make sure that it has my name, Hyoungshick Kim, marked clearly on it.
3. You should submit your work even if you know it's incomplete or incorrect; such work tells me what you most need help with.

Supervision Notes

· Sequence alignment (I)

· Sequence alignment (II)

· Phylogenetics

· Hidden Markov Model

Assignments

· Assignment I

· Assignment II

· Assignment III

· Assignment IV

Other resources

· Official course page

· Sequence alignment softwares

- NeoBio (http://neobio.sourceforge.net/)

- EMBOSS-Align (http://www.ebi.ac.uk/Tools/emboss/align/index.html)

- Global Alignment (http://dimacs.rutgers.edu/dci/2005/GlobalAlignment.html)

· Useful articles

- Aligning DNA Sequences Using Dynamic Programming (http://www.acm.org/crossroads/xrds13-1/dna.html)

- Four Russians’ algorithm