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Genetic analysis and molecular evolution, fall 2012

Lecturer

Sirkka-Liisa Varvio

Scope

4-6 cu.

Type and time schedule

Lectures, home-exercises, computer class sessions.

Weeks 36-42, Tuesday 14-16, Thursday 14-16 B120 and computer class C128 Tuesday 16-18 and negotiable additional sessions.

Prerequisites

Basic probabilistics and interest in bio-applications of statistics. This course is suitable for students with planned orientation to biometry and bioinformatics and also for other students interested in all-round-education on biological applications of statistical inference. In HU Bioinformatics Master´s program (MBI) this is one of the optionally compulsory courses and in Aalto-MBI a compulsory course.

Short description

Characteristics of molecules and inheritance as statistical and computational challenges.
Sequence databases - how to retrieve sequence information and use it for comparative purposes - multiple sequence alignment.
The neutral theory of molecular evolution - sequence evolution models and phylogeny inference.
Basics of genetic inheritance and population genetics.

4cr Exam, based on lectures and assignments. Exam will be in computer class and you have access to all material.
6cr Participating also in the Journal Club.

Week 1

Thu 6.9
14-16, B120
First lecture.pdf

Week 2

Tue 11.9,
14-16, B120
Modelling sequence evolution.pdf
16-18, C128 (=computer class), This is for those who have not worked with sequence databases before. http://www.ncbi.nlm.nih.gov/.
Those who are familiar with NCBI-database working can (probably) do the initial part of Assignment 1 (1a, below) without attending this computer class session.
Assignment 1a - Instructions for collecting data from NCBI.pdf, Assignment 1 - Initial dataset.txt,
Read these: NCBI BLAST.pdf, Multiple sequence alignment.pdf

Thu 13.9
14-16, B120, Sequence relationships - Phylogenetic trees.pdf, Distance matrix phylogenies as a handout-copy.

Week 3

Tue 18.9, 16-18, C128
Assignment 1b - Phylogenetic trees.pdf, http://www.megasoftware.net/, http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html.

Thu 20.9, 14-16, C128
Assignment 1c - Substitution patterns and rates.pdf

Useful Phylo tutorial.pdf, http://tolweb.org/tree/, http://www.timetree.org/, Today in Nature.pdf,
Assignment 1 - Instructions for writing the report.pdf

Reserve time for further personal advise from here: http://doodle.com/6frkpgknw7m7exnr

Week 4

Tue 25.9, 14-16, B120
Topics on molecular evolution will be completed later. Now we switch to topics on population genetics so that there will be enough time for assignment 2.
Inheritance, pedigree analysis.pdf, The basic model in population genetics, Hardy-Weinberg.pdf
Assignment 2a.pdf

Thu 27.9, 14-16, B120
Population genetics continues.
http://www.radford.edu/~rsheehy/Gen_flash/popgen/, The basic selection model and Random genetic drift.pdf
Assignment 2b.pdf

Week 5

Tue 2.10, 14-16, B120 and 16-18 C128
The basic selection model and Random genetic drift continues.
Computer simulations. Assignment 2c.pdf

Week 6

Tue 9.10, 16-18, C128
Assignment 1 presentations.

Thu 11.10, 12.30-14, B120, 14-16, C128. Note the extra time 12.30-14 (the slot is free for this lecture because there will not be Algorithms for bioinformatics lecture.)
Last lecture.pdf
Assignment 1 presentations continue.
Assignment 2c presentations.
Assignment 2a Solutions.pdf
Assignment 2b Solutions.pdf

Week 7

EXAM in computer class C128, Tue 16. October, 12-20.

Course Moodle-area 

Journal club

Read instructions here.pdf

 

Tree_of_life_1.pdf, Human_pop_evo_1.pdf, Human_pop_evo_3.pdf, Human_pop_evo_6.pdf, Human_pop_evo_7.pdf, Disease_1.pdf, Disease_2.pdf, Disease_3.pdf, Disease_4.pdf, Animals_2.pdf, Animals_3.pdf, Bacteria_2.pdf, Virus_1.pdf, Virus_2.pdf, General_1.pdf, General_2.pdf, General_4.pdf

 

Extra assignment 1.pdf

Registration

EXAM 16102012.pdf, UK_MEX_FIN_data.txt

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