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--- teaching:2017summer:gr [2017/07/14 15:35]
+++ teaching:2017summer:gr [2020/02/14 09:07] (current)
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+====== Algorithms for Genome Rearrangement (2V + 2Ü) ======
+| 392189/92 | Dörr | Summer 2017 | Fr 09:00 - 10:15 (Ü), Fr 10:15 - 11:45 (V) in U10-146 | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=89696111|ekvv]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=89696167|ekvv]] |
+===== Content =====
+Many questions in molecular biology, phylogenetics, and biomedicine can be approached through comparison of two or more genomes. However, a global alignment of multiple large genomes is often infeasible or comes at great expense. It is more efficient to compare genomes on a higher level of abstraction, as given by the succession of single-copy genes or other kinds of unique genomic markers on the chromosomal sequences.
+In this course, various models of higher level genome comparison are discussed. We start with the classical reversal distances which are measures to study chromosomal sequences only permuted by inversions. We then continue by discussing distances such as SC/J or DCJ, and a general rearrangement distance. It then follows a discussion of methods that solve the problem of comparing sequences with unequal gene/marker content. We will also study methods for the reconstruction of ancestral genomes.
+Algorithms discussed in this course are mostly combinatorial by nature, similar to the sequence analysis course.
+This course is taught in German or English if needed.
+===== Conditions for participation, prior knowledge =====
+Required: Algorithms and Data Structures (or comparable)\\
+Recommended: Sequence Analysis and Foundations of Genome Research
+===== Inversion Visualization Software =====
+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 {{https://gi.cebitec.uni-bielefeld.de/_media/teaching/2017summer/Inversion.zip|here}}.
+**Usage:** ''java InversionVisualisation file_name''
+**For example:** ''java InversionVisualisation example.txt''
+The input must be a signed permutation in one line, the numbers separated with a <tab>. There is an example in the provided archive.
+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.
+===== Schedule =====
+| **Date** | **Topic(s)** | **Notes** | **Exercises** | **Remarks** |
+| 21.04.2017 | Genome rearrangements, unsigned reversal distance| {{ notes01.txt | 01 }} | {{ exercise01.pdf | 01 }} **3, 4**| lit.: {{ https://link.springer.com/article/10.1007/BF01188586 |1}}, {{ http://epubs.siam.org/doi/10.1137/S0097539793250627 |2}}, {{ pevzner_chapter10.pdf |3}} |
+| 28.04.2017 | Unsigned (part II) and signed reversal distance| {{ notes02.txt | 02 }} | {{ exercise01.pdf | 01 }} **1, 2**, {{ exercise02.pdf | 02 }} ** 1 ** | lit.: {{ InversionBergeron.pdf |4}}, {{ http://dl.acm.org/citation.cfm?id=300515.300516 | 5 }} |
+| 05.05.2017 | Signed reversal distance (part II) | {{ notes03.txt | 03 }} | {{ exercise02.pdf | 02 }} **2**, {{ exercise03.pdf | 03 }} | lit.: {{ InversionBergeron.pdf |4}}, {{ http://dl.acm.org/citation.cfm?id=300515.300516 | 5 }} permutations: {{pi_2.txt|π^2}}, {{pi_3.txt|π^3}}, {{fortress.txt|fortress}}, {{permutation_ex02.2.txt|Ex. 02.2}} |
+| 12.05.2017 | Sorting by (signed) reversals | {{notes04.txt |04}} | {{ exercise04.pdf | 04 }} **for 3, only draw OV(π)** | lit.: {{ InversionBergeron.pdf |4}},{{http://www.sciencedirect.com/science/article/pii/S0166218X06003751|6}} |
+| 19.05.2017 | Algebraic Theory for Genome Rearrangements | {{notes05.txt |05}} | {{ exercise05.pdf | 05 }} | lit: {{ medianis_algebraic_theory.pdf|7}}, {{http://ieeexplore.ieee.org/iel5/7760/21327/00989776.pdf |8}}, {{teaching:2015summer:730lecture-algebraic.pdf|9}} |
+| 26.05.2017 | Double-Cut-and-Join (DCJ)| {{notes06.txt |06}} | {{exercise06.pdf| 06 }} | lit: {{Bergeron_DCJ.pdf | 10}} |
+| 02.06.2017 | **Guest lecture by Eyla Willing**: DCJ with insertions and deletions | | {{exercise07.pdf| 07 }}| lit: {{http://online.liebertpub.com/doi/abs/10.1089/cmb.2011.0118 | 11}} |
+| 09.06.2017 | Breakpoint distance with duplicates |{{notes08.txt|08}} | {{exercises08.pdf| 08}} | lit: {{http://online.liebertpub.com/doi/abs/10.1089/cmb.2008.0061 | 12}}, {{bryant_2000.pdf|13}} |
+| 16.06.2017 | Family-free genome comparison| {{notes09.txt | 09}} | {{exercise09.pdf | 09 }} | lit: {{https://pub.uni-bielefeld.de/download/2902049/2902050|14}}, {{https://almob.biomedcentral.com/articles/10.1186/s13015-015-0041-9|15}} |
+| 23.06.2017 | Genome median problem| {{notes10.txt | 10}} | {{exercise10.pdf | 10}}| lit: {{https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-120|16}}, {{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3887456|17}}  |
+| 30.06.2017 | Genome halving | {{notes11.txt|11}} | {{exercise11.pdf|11}} **3** | lit: {{mixtacki_2008.pdf|18}} |
+| 07.07.2017 | Ancestral genome reconstruction I | {{notes12.txt|12}} | {{exercise11.pdf|11}} **1, 2**| lit: {{https://academic.oup.com/gbe/article/9/5/1312/3200386/DeCoSTAR-Reconstructing-the-Ancestral-Organization| 19}}|
+| 14.07.2017 | Ancestral genome reconstruction II | {{notes13.txt|13}} | {{exercise12.pdf|12}} | lit: {{https://doi.org/10.1093/bioinformatics/btt527|20}}, {{https://pub.uni-bielefeld.de/publication/2909213|21}}, {{https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S19-S11|22}}, {{http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000123|23}} |
+| 21.07.2017 | Exam prep Q&A| -- | | |
+| 28.07.2017 | Oral exam | -- | | |
+----
+Back to [[:teaching|Teaching]]

Genome Informatics

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