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


|392109/10 | Pedro Feijão | Fr 8:45-10:15/Fr 10:15-11:45 in T2-208 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=49568200|ekvv (V)]] | [[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=49568249|ekvv (Ü)]] |

==== 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/2014summer/gr?action=AttachFile&do=get&target=Inversions.zip|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 black 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** |
| 10.10.2014 | Introduction, logistics /  Genome rearrangements - Reversals 1 | {{ 441lecture1-reversal.pdf | Slides }} |  {{ 441uebung-01.pdf | Exercises }} |
| 17.10.2014 | Genome rearrangements - Reversals 2  | {{ 441lecture2.pdf | Slides }} |
| 24.10.2014 | (no class) | --- |
| 31.10.2014 | Genome annotation I: Introduction to HMMs | {{ 441ExerciseList2.pdf | Exercises }} |  {{ 441ExerciseList2.zip | ExerciseList2.zip }} | Solve 1,2(b), 3(b)|
| 07.11.2014 | Genome annotation II: Finding protein-coding genes | --- |
| 14.11.2014 | Reversals without Hurdles and Fortresses | {{ 441Reversal-Mixtacki.pdf | Slides }} |  {{ 441uebung03.pdf | Exercises }} |
| 21.11.2014 | Genome rearrangements - DCJ operation |   {{ 441lecture04.pdf | Slides }} |  {{ 441uebung-4.pdf | Exercises }}|
| 28.11.2014 | Physical mapping |  [[https://courses.cs.washington.edu/courses/cse421/10au/lectures/PQ.pdf|PQ-tree (University of Washington)]] | {{ 441uebung-05.pdf | Exercises }} |
| 05.12.2014 | Sequence assembly I | [[http://www-ab.informatik.uni-tuebingen.de/teaching/ws09/bioinformatics-i/11-assembly.pdf|Lecture notes by Daniel Huson]] |  {{ 441uebung-6.pdf | Exercises }}|
| 12.12.2014 | Sequence assembly II | [[http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html|Main Reference]] | {{ 441uebung-07.pdf | Exercises }}|
| 19.12.2014 | Sequence assembly III | [[http://bib.oxfordjournals.org/content/5/3/237.full.pdf|Comparative genome assembly]] | {{ 441uebung-08.pdf | Exercises }}|
| 09.01.2015 | RNA sequencing I - EST and RNA-Seq Assembly | [[http://www.ncbi.nlm.nih.gov/pubmed/12169546|Ref 1]] |  [[http://www.nature.com/nrg/journal/v12/n10/full/nrg3068.html|Ref 2]] |  {{ 441uebung-09.pdf | Exercises }}|
| 16.01.2015 | RNA sequencing II - Microarrays | [[http://bioinformatics.oxfordjournals.org/cgi/reprint/19/suppl_2/ii156.pdf|Ref 1]] |  {{ 441uebung-10.pdf | Exercises }}|
| 23.01.2015 | Gene Clusters |  {{ 441Uno, Yagiura - 2000 - Fast Algorithms to Enumerate All Common Intervals of Two Permutations.pdf | Ref 1 }} | {{ 441uebung-11.pdf | Exercises }}|
| 30.01.2015 | Gene Clusters II |{{ 441Heber, Stoye - 2001 - Finding All Common Intervals of k Permutations.pdf | Reference }} | {{ 441uebung-12.pdf | Exercises }}  |
| 06.02.2015 | Metagenomics | -- |

==== Examination dates ====
Back to [[:teaching|Teaching]]