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Biometry and bioinformatics II, fall 2013


Sirkka-Liisa Varvio

Scope, type, prerequisites and relationships to other courses

5-10 cr, intermediate/advances studies.

At least basic courses on probability and statistical inference.  Biometry and bioinformatics I  (or knowledge/practical skills on working with biological sequence databases and sequences from some other course).

In previous years there have been the courses Genetic analysis and molecular evolution, Phylogeny inference and data analysis. These courses are no more in teaching curriculum, instead the course Biometry and bioinformatics II covers the topics in those past courses. Contents will be almost completely newly scheduled, and because of only slight overlap, those who have taken the previous courses can now attend this course. 

The course consists of lectures, discussions, tutorial lectures during computer sessions, assignments initiated during computer session (completed during student´s own, additional, time). The spirit of the course is  learning by doing (data-analysis) and reading scientific papers, rather than listening lectures.

Lectures / computer class sessions

I period, 5 cr: 24.9 - 17.10 Tuesday and Thursday 14-16 in room B120 and 16-18 in computer class C128; 9.10. and 16.10. also Wednesday 14-18 in C128.
II period, 2-5 cr: Project work, time schedule negotiable. Project(s) are extensions of course assignments. Note also this seminar as one kind of an extension of BB_II.

Content scheme

Characteristics of molecules and molecular evolution as statistical and computational challenges. Sequence evolution models,  phylogeny inference by distance matrix methods (such as the neighbor joining algorithm), maximum parsimony methods, maximum likelihood methods, Bayesian methods. These themes are accompanied by data analysis. 
The broad goal is to provide understanding of life (such as the tree, or network, of life) at the levels of species and genomes - through molecular information.

Course grade

Passing the course with grade 1: Assignments done and half of the maximum points from the exam (Note that half of the maximum points is the general rule for passing a course by grade 1. As about half of the course consists of working in computer class, accompanied with assignments, this course is not a standard lecture course from which assignments/exercises might give some extra bonus to a final grade => Assignments and exercises are compulsory. It is possible to perform assignments and exercises without participating the lectures/computer class sessions (note, however, that these sessions give the tutorials.)
Passing the course with grade 5
Assignments and exercises done and 5/6  of the maximum points from the exam (5/6 is the general rule for passing a course by grade 5.)
Passing the course by grades 2-4: Exam points between the above extremes.

Week 1

Thu 26.9, 14.15 - 16 in B120, 16 - 18 in C128 


Week 2

Tue 1.10, 14.15 - 17 in C128

• Phylogeny methods - parsimony, ML, bayesian_ (some but not yet all slide editing done).pdf 

MrBayes-softwareMrBayes Manual 3.1.pdf, Original MrBayes paper.pdf, MrBayes Commands.pdf, This is useful clarification.pdf
Traditional and Bayesian phylogeny estimation.pdf


Link to data-conversion (use this, or use Clustal, for obtaining a nexus-format from the data so that it can be submitted to MrBayes)
Link to choosing a model
(note also model choice option in MEGA5)  Modeltest.pdf

Move the file (the training file primates.nex) to Z, and when strating MrBayes: execute z:\primates.nex

Thu 3.10, 15.00 - 18 in C128

Week 3

Tue 8.10, 14.15 - 17 in C128

Wed 9.10, 14.15 - 18 in C128  

Teacher: Virginia Brilhante from Biomedicum, Research Program for Molecular Neurology.
Amino acid evolutionary diagnosis of function-altering mutations in silico by using the softwares SIFT (Sorting Intolerable From Tolerable) and PolyPhen (prediction of functional effects of human nsSNPs).


Assignment 3 material:
, cs2PatientExomeVariantDataSample-1.txt

Thu 10.10, 14.15 - 18  in C128

Working for assignments

Week 4 

Wed 16.10   

13.00 - 15.45 in C128 results from assignments

Fri 18.10

EXAM, 10-19.30 in C128. You can choose a time slot. It is good to reserve ~4 hours, but there will not be a time limit. However, 19.30 is the submission deadline (the class will be closed).

period II ->

Assignments fore more credits will appear here.
Deadlines for submitting them: during II-IV periods.
Topics will be phylogenies, molecular evolution.
If you have something special in mind, such us focusing on human-, animal-, virus-, bacteria-data (etc.), contact lecturer in order to get a tailored project.

Note also this seminar as one kind of an extension of BB_II. 

Topics for additional credits, 1 cr is ~5 page essay from a topic based on a reference from the list.
No deadline and no limit to the number of essays. Submissions to course Moodle or by email to sirkka-liisa.varvio at

Phylo_1.pdf, Phylo_2.pdf, Phylo_3.pdf, Phylo_4.pdf, Phylo_5.pdf, Phylo_6.pdf, Phylo_7.pdf, Phylo_8.pdf, Phylo_9.pdf, Phylo_10.pdf



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