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Biometry and bioinformatics I, fall 2013

Lecturer

Sirkka-Liisa Varvio 

Scope, type and goal

2-5 cr

Submitting assignments during the two course weeks = 2 cr.  Pass/fail.
Extra assignments after the course = 1-3 additional credits.

This short course gives very basic practicals for working with biological sequence data and databases: making sequence queries ("blasting"), introduction to different kind of sequence databases, aligning seqs and clustering them. 

If you have taken the course Genetic analysis and molecular evolution previously (or know how to work with biological sequence databases from some other previous course), then Biometry and bioinformatics I is not for you and you can start from Biometry and bioinformatics II.
However, if you already know how to work with sequence data /sequence databases (for example on the basis of Genetic analysis and molecular evolution), you can take this course  (without a need to participate the computer sessions) as assignments will not be the same as previously.

The contents of this BBI has previously been the introductory part of the course Genetic analysis and molecular evolution. If you have taken this old course (or know the abovementioned basics from some other course),
- you can do the assignments and get the credits (the assignments will not be identical with those you have already done in Genetic analysis and molecular evolution)
- but you need not come to attend the sessions, starting Tuesday, 10.9, 14.15 - 17.00 in C128. In fact: do not come because the course will be very big, 24 computers, 38 students.
So, if this address http://www.ncbi.nlm.nih.gov/ is familiar, don´t come, just wait for the assignments to appear in course webpage.

 


Computer session 10.9, C128, 14.15 - 17

Computer session 12.9, C128, 14.15 - 18

We check your proceeding with the tutorial example.
Introduction to sequence alignment by Clustal (installed in C128); also http://mafft.cbrc.jp/alignment/server/ will be introduced.
Multiple sequence alignment.pdf

Introduction to clustering by http://www.megasoftware.net/ (installed in C128).

Assignment 1_ BBI.pdf , gene.txt

Computer session 17.9,  C128, 14.15 - 17

Computer session 19.9, C128 14.15 - 18

Working with assignments 1 and 2. 


Extra assignments, submission deadline 31.12.2013


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