BIOL3014
- Textbook: Biological sequence analysis, Durbin, Eddy, Krogh and Mitchison.
- Learning Guide
[HTML]
[MSWord]
- VISAC: You may access VISAC 24/7 to do your Practicals except at
times when it is booked by other classes. Check
here
for times when VISAC is booked by other classes.
Note: If you experience problems with VISAC workstations, please
report them immediately by calling 56000 from the phone in VISAC.
- Handy links for help with Python Programming:
- Week 1: Textbook Reading- Ch 1, p1-11; Ch 11, p299-301.
- Tutorial 1: Learning Python
- Tutorial 1 overview, linux commands [pdf]
- Tutorial introduction to python [pdf]
- Reference for python [pdf]
- Human mitochondrial genome [text file]
- Week 2: Textbook Reading- Ch 2
- Week 3: Textbook Reading- Ch 3 p. 46-69
- Week 4: Textbook Reading- Ch 3, p. 46-72.
- Week 5: Textbook Reading- Ch 3 p. 61-72; Ch 5, p. 100-133.
- Week 6: Textbook - Ch7 p160-179, Ch8 p192-206
- Week 7: Chapter 18 from Felsenstein: Inferring Phylogenies
Also pages 9-15 from the original MrBayes manual
- Project: The Transmembrane Cup
- Week 8: Chapter 4 from Nei and Kumar: Molecular Evolution and Phylogenetics
Also the PAML manual has lots of useful information
The evolution of opsins is described in Yokoyama's 2002 paper
The tutorial uses "codeml" from PAML, precompiled for ViSAC. [The source code is here]
- Week 10: Reference: Baldi and Hatfield: DNA Microarrays and Gene Expression
- Week 11: Textbook Reading- Ch 6 and Ch 11
- Week 12: Textbook Reading- Ch 10
- Week 13: Review
- Final Exam
- Date: Tuesday, 8th November, 2005
- Time: 11:15 AM
- Place: Room 224, GP South
- Format: Mainly short-answer questions. Expect to do some (simple) calculations, and draw the odd diagram.