====== Algorithms in Genome Research ======
\\ 


|392109/10 | Jens Stoye, Annelyse Thévenin, Pedro Feijão | Fr 10:15-11:45/Fr 8:45-10:15 in U10-146 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=37773620|ekvv]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=37773726|ekvv]] |

==== Contents: ====
This class covers the basic algorithmic techniques used in the computational analysis of genome and post-genome data. This includes algorithms for genomic mapping and assembly, methods for functional genome annotation (gene finding and gene function prediction), algorithms for the analysis of DNA microarrays and mass spectra, methods and models for protein structure prediction, and algorithms for comparative genomics. 



==== Literature: ====
The page [[teaching:alggrliterature|AlgGRLiterature]] contains many links to the original literature. 



==== Software ====


=== Reversals and BP Graph ===
Prof. Istvan Miklos, from the [[http://renyi.hu/staff/bioinf.html|Bioinformatics Group]] in Alfréd Rényi Institute in Budapest, kindly shared his visualization software for the Breakpoint Graph. It is written in Java, and you can download it [[http://wiki.techfak.uni-bielefeld.de/gi/Teaching/2013winter/algGR?action=AttachFile&do=get&target=Inversions.tar.gz|here]]. 

**Usage:** ''java InversionVisualisation file_name'' 

**For example:** ''java InversionVisualisation permutation.txt'' 

The input must be a signed permutation in one line, the numbers separated with a TAB. There are some examples in the package.  

Select the reality edges on which the reversal should act, and press the button Mutate. You can go forward and backward in the list of generated genomes, and you can delete any of them, too. 



==== Time table: ====

| **Date** | **Topic** | **Exercises** | **Name** |
| 11.10.2013 | Introduction, logistics | (none) | all |
| 18.10.2013 | (no class) | (none) | --- |
| 25.10.2013 | Genome rearrangements - Reversals 1 | {{ 702exercisesReversals-v2.pdf | Exercises }} |  {{ 702lecture1-handout.pdf | Slides }} | Pedro Feijão |
| 01.11.2013 | (no class) | --- | --- |
| 08.11.2013 | Genome rearrangements - Reversals 2 | {{ 702exercisesReversalsB.pdf | Exercises }} | {{ 702lecture2-handout.pdf | Slides }} | Pedro Feijão |
| 15.11.2013 | Genome rearrangements - DCJ operation | {{ 702exercisesDCJ.pdf | Exercises }} |  {{ 702lecture3-handout.pdf | Slides }} | Pedro Feijão |
| 22.11.2013 | Multiple Genome Rearrangements and Breakpoint Models |  {{ 702ExercisesMGR.pdf | Exercises }} | {{ 702lecture4-handout.pdf | Slides }} | Pedro Feijão |
| 29.11.2013 | Assembly 1 | {{ 702exercises05-Assembly1.pdf | Exercises }} | Annelyse Thévenin |
| 06.12.2013 | Assembly 2 | {{ 702exercises06-Assembly2.pdf | Exercises }} | Annelyse Thévenin |
| 13.12.2013 | Genomic similarities 1 | {{ 702exercises07-Assembly3CG1.pdf | Exercises }} | Annelyse Thévenin |
| 20.12.2013 | Genomic similarities 2 | {{ 702exercises08-CG2.pdf | Exercises }} | {{ 702lecture8-duplication.pdf | Slides1 }} | {{ 702lecture8-FF.pdf | Slides2 }} | Annelyse Thévenin |
| 10.01.2014 | RNA sequencing | {{ 702exercises09RNASeq.pdf | Exercises }} | Jens Stoye |
| 17.01.2014 | Computational Systems Biology | {{ 702exercises10SystemsBiology.pdf | Exercises }} | Jens Stoye |
| 24.01.2014 | Haplotype inference | {{ 702exercises11HaplotypeInference.pdf | Exercises }} | Jens Stoye |
| 31.01.2014 | SNP-disease association mapping | {{ 702exercises12AssociationMapping.pdf | Exercises }} | Jens Stoye |
| 07.02.2014 | Metagenomics, astrobiology | -- | Jens Stoye |

==== Organisational Matters: ====
Together with the practical course "Bioinformatics Applications in Genome Research" in the following summer semester, this lecture forms the master module [[http://www.zfl.uni-bielefeld.de/studium/module/techfak/modulhandbuch/#algorithmen_genomforschung|Algorithms in Genome Research]].\\ The exercises will not be corrected or graded, but presence and activity during the exercise hours is expected. Credit points will be given based on an oral exam at the end of the semester. 



==== Examination dates ====

| Oral exam | 11.02.2014 or 31.03.2014 | Contact Heike Samuel for individual appointments |Back to [[:Teaching|Teaching]]