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:
  • Python Language Reference Manual.
  • Python Tutorial.

• 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
  • Lecture 3: Pairwise Alignment I
  • Lecture 4: Pairwise Alignment II
  • Tutorial 2: Probability Theory [tarfile]

• Week 3: Textbook Reading- Ch 3 p. 46-69
  • Lecture 5: Probability and Markov Models I
  • Lecture 6: Hidden Markov Models I
  • Tutorial 3: Pairwise Sequence Alignment [tarfile]

• Week 4: Textbook Reading- Ch 3, p. 46-72.
  • Lecture 7: Hidden Markov Models II
  • Lecture 8: Hidden Markov Models III
  • Tutorial 4: HMMs: Viterbi and Forward Algorithms [tarfile]

• Week 5: Textbook Reading- Ch 3 p. 61-72; Ch 5, p. 100-133.
  • Lecture 9: Hidden Markov Models IV
  • Lecture 10: Hidden Markov Models V
  • Tutorial 5: Profile HMMs [tarfile]

• Week 6: Textbook - Ch7 p160-179, Ch8 p192-206
  • Lecture 11: Phylogenetics (parsimony and distance)
  • Lecture 12: Phylogenetics (probabilistic)
  • Tutorial 6: Phylogeny
    • [assignment]
    • [data file]
    • [Fixed python module]
    • Due 8th September

• Week 7: Chapter 18 from Felsenstein: Inferring Phylogenies
  Also pages 9-15 from the original MrBayes manual
  • Lecture 13: Phylogenetics (Bayesian analysis)
  • Lecture 14: Recombination and other unpleasantness
  • Tutorial 7: Recombination and Bayes
    • [assignment]
    • [Attached figure: PostScript without preview]
    • [full-length data file]
    • [variable sites from data file]
    • [You will also need: the version of sequence.py that can read gaps]
    • Due 15th September

• Project: The Transmembrane Cup
  • Project description handout
  • Project files (tarred)
  • Due 13th October

• 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]
  • Lecture 15: Detecting natural selection at the molecular level
  • Lecture 16: Case studies in selection
  • Tutorial 8: Selection
    • [assignment]
    • [Globin sequences]
    • [Opsin sequences]
    • [You will also need: codeml and some extra files from PAML: in /HPC/groups/Courses/BIOL3014/select for ViSAC executables]
    • Due 23rd September, if you're sensible

• Week 10: Reference: Baldi and Hatfield: DNA Microarrays and Gene Expression
  • Lecture 17: Microarray data issues B&H: p49-51, 53-61, 68
  • Lecture 18: Cluster analysis B&H:p73-87
  • Tutorial 10: Microarrays
    • [assignment]
    • [python code]
    • [data set]
    • Due 13th October

• Week 11: Textbook Reading- Ch 6 and Ch 11
  • Lecture 19: Multiple Sequence Alignment
  • Lecture 20: Motif Discovery
  • Gary Stormo's paper on DNA motifs
  • Tutorial 11: Motif Discovery [tarfile]

• Week 12: Textbook Reading- Ch 10
  • Lecture 21: Motif-based HMMs
  • Lecture 22: RNA folding
  • Tutorial 12: RNA folding (no programming required) [postscript] [PDF]
• Week 13: Review
  • Lecture 23: Course Review
  • Transmembrane Cup Results

• 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.