392131 Variation calling challenge (Pj) (WiSe 2012/2013)

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Project: Variation calling challenge, 2 ECTS, 4*2 hours

You are given reference genome A and simulated short read data D from genome B. Genome B is
variant of A with some simulated SNPs, and short and large indels. The task is to reconstruct B'
from A and D such that B' is as close to B as possible. The closeness is measured by the alignment
score of B’ and B; the alignment is produced by projecting the alignment of B’ to A, given by
you, to the alignment of B’ to B through the original generated alignment of A to B. You can use
any tools available to produce sequence B’ and its alignment to A.
Dataset is provided by the lecturer. Project lasts 4 weeks and it can be done in small teams.
Guidance is offered 2 hours per week.

Requirements for participation, required level

This class will be given in English.

Teaching staff

Dates ( Calendar view )

Frequency Weekday Time Format / Place Period  
by appointment n.V. 10-12   05.11.-01.12.2012

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Subject assignments

Module Course Requirements  
39-M-Inf-AG Algorithms in Genome Research Algorithmen in der Genomforschung Bioinformatische Anwendungen in der Genomforschung Study requirement
Student information

The binding module descriptions contain further information, including specifications on the "types of assignments" students need to complete. In cases where a module description mentions more than one kind of assignment, the respective member of the teaching staff will decide which task(s) they assign the students.

Degree programme/academic programme Validity Variant Subdivision Status Semester LP  
Bioinformatik und Genomforschung / Bachelor (Enrollment until SoSe 2011) Individueller Ergänzungsber Wahl 5. 2 unbenotet  
Bioinformatik und Genomforschung / Master (Enrollment until SoSe 2012) Algorithmen in der Genom Wahlpflicht 1. 2 benotet  
Bioinformatik und Genomforschung / Promotion Indiv. Erg. Wahl unbenotet  
Molekulare Biotechnologie / Diplom (Enrollment until SoSe 2004)   HS
Molekulare Biotechnologie / Master (Enrollment until SoSe 2012) Individuelle Ergänzung Wahl 1. 2 unbenotet  
Naturwissenschaftliche Informatik / Diplom (Enrollment until SoSe 2004) Biologie   HS
Naturwissenschaftliche Informatik / Master (Enrollment until SoSe 2012) Projekt II Wahlpflicht 1. 2 benotet  
No more requirements
No eLearning offering available
Address:
WS2012_392131@ekvv.uni-bielefeld.de
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Additional notes on the electronic mailing lists
Last update basic details/teaching staff:
Friday, December 11, 2015 
Last update times:
Friday, September 7, 2012 
Last update rooms:
Friday, July 20, 2012 
Type(s) / SWS (hours per week per semester)
project (Pj) / 2
Department
Faculty of Technology
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33919984