392131 Variation calling challenge (Pj) (WiSe 2012/2013)
Contents, comment
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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
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This class will be given in English.
Teaching staff
Dates ( Calendar view )
| Frequency | Weekday | Time | Format / Place | Period |
|---|
Subject assignments
| Module | Course | Requirements | |
|---|---|---|---|
| 39-M-Inf-AG 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 |
- Address:
- WS2012_392131@ekvv.uni-bielefeld.de
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- Notes:
- 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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