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— teaching:2015winter:alggr [2020/02/14 09:07] (current)
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 +====== Algorithms in Genome Research ======
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 +|392109/10 | Pedro Feijão, Jens Stoye | Fr 8:​45-10:​15/​Fr 10:15-11:45 in U10-146 |[[http://​ekvv.uni-bielefeld.de/​kvv_publ/​publ/​vd?​id=59466392|ekvv (V)]] | [[http://​ekvv.uni-bielefeld.de/​kvv_publ/​publ/​vd?​id=59466765|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. ​
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 +
 +
 +==== Literature: ====
 +The page [[teaching:​alggrliterature|AlgGRLiterature]] contains many links to the original literature. ​
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 +
 +
 +==== 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&​amp;​do=get&​amp;​target=Inversions.zip|here]]. ​
 +
 +**Usage:** ''​java InversionVisualisation file_name'' ​
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 +**For example:** ''​java InversionVisualisation permutation.txt'' ​
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 +The input must be a signed permutation in one line, the numbers separated with a TAB. There are some examples in the package.  ​
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 +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** |
 +| 23.10.2015 | Introduction,​ logistics (Pedro, Jens) | -- |
 +| 30.10.2015 | Genome Assembly I (Jens) | {{ 992exercises01Assembly.pdf | Exercises 1 }} |
 +| 06.11.2015 | (no class) | -- |
 +| 13.11.2015 | Genome Assembly II (Jens) | {{ 992exercises02HtsAssembly.pdf | Exercises 2 }} |
 +| 20.11.2015 | Transcriptomics,​ RNA-Seq (Jens) | {{ 992exercises03RNASeq.pdf | Exercises 3 }} |
 +| 27.11.2015 | RNomics (Pedro) | {{ 992exercises04RNAfolding.pdf | Exercises 4 }} |
 +| 04.12.2015 | Mass Spectrometry for Proteomics and Metabolomics (Jens) | {{ 992exercises05MassSpec.pdf | Exercises 5 }} |
 +| 11.12.2015 | Computational Systems Biology (Jens) |{{:​teaching:​2015winter:​exercises06systemsbiology.pdf| Exercises 6}} |
 +| 18.12.2015 | Genome Annotation (Jens) | {{:​teaching:​2015winter:​exercises07genomeannotation.pdf| Exercises 7}}|
 +| 08.01.2016 | Sorting By Reversals I (Pedro) |{{:​teaching:​2015winter:​exercises08reversalsorting.pdf| Exercises 8}} |
 +| 15.01.2016 | Sorting By Reversals II (Pedro)|{{:​teaching:​2015winter:​exercises09reversal_ii.pdf| Exercises 9}} |
 +| 22.01.2016 | Sorting by DCJ (Pedro) |{{:​teaching:​2015winter:​exercises10dcj.pdf| Exercises 10}} |
 +| 29.01.2016 | Reconstruction of Ancestral Genomes (Pedro) | {{:​teaching:​2015winter:​exercises11ancestralreconstruction.pdf|Exercises 11}}|
 +| 05.02.2016 | Haplotype Inference (Pedro) |{{:​teaching:​2015winter:​exercises12haplotype.pdf|Exercises 12}} |
 +| 12.02.2016 | Metagenomics,​ Astrobiology (Pedro) | -- |
 +==== Examination dates ====
 +Oral exams will be on 26.02.2016. Please make an appointment with the secretary in U10-151, Heike Samuel. ​
 +
 +If necessary, a second oral exam can be scheduled on an individual basis until end of March 2016. 
 +
 +Back to [[:​teaching|Teaching]] ​
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 +