Thursday, July 9th

Morning 9.30am

Solve account questions

Lecture: What is Bioinformatics?

Why is molecular evolution important for Bioinformatics
Databanks available at NCBI (Topic #1)

- Assignments #1

Afternoon: lecture 1.30 pm

Overview on Phylogenetic Reconstruction:
From Databank Searches to Tree Building;
Types of Homology - why should you care? (Topic #2a)

15 min break

From Gene to Protein (Topic 2b) ORF finding, Genescan, Genemachine and Workbench exercises

Friday

Morning 9am

Lecture: (Topic3)

Homology assessment: When are two sequences homologous? z-values, PRSS, Blast and Psi-Blast

Using Position Specific Scoring Matrices (PSSMs) to search microbial genomes.

- Assignment #3

Afternoon 1.30 pm:

Lecture:

Multiple Sequence Alignments (topic #4),

- Start Assignments #4 (topic #4)

Monday

Morning 9 am

Lecture and Demonstrations:

Distance trees with clustalw, treeview, rooted and unrooted trees

Bootstrap analyses

Some other tree-building programs – phyml, puzzle trees and ml mapping (Task 7)

- Finish Assignmens on Alignment #4 Task 2, 3, and 4

- Assignments #5

- Assignments #7 Task 1 (2 if time)

Afternoon 1.30 pm:

Lecture and Demonstrations:

Comparative genome analyses (Task 6)

-Assignments #6

Tuesday

Morning:

Lecture and demonstration: Swiss Protein data bank viewer (Task 8)

Exercises 8A and 8B

Afternoon:

Aligning structure with SPDBV and structure based alignments

Exercises 8C and 8D

Wednesday, July 15th

Morning:
Bayesian probabilities, Markov Chain Monte Carlo approaches, Trees with MrBayes.

Determing sites under positive selection.

General discussion

Afternoon:

EXAM

Exams starts at 1pm!