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Algorithms in Comparative Genomics (2V + 2Ü)

392189/92 Dörr Winter 2018 Th 09:00 - 10:15 (Ü), Th 10:15 - 11:45 (V) in U10-146

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 breakpoint distance, followed by other simple measures such as SC/J and DCJ. The reversal distance will be discussed, and a general genome rearrangement distance. 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 English.

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 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 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 Notes Ex. Remarks
11.10.2018 – no class – – –
18.10.2018 Genome rearrangements, signed reversal distance, part I 01/02 01 lit.: 1, 2
25.10.2018 Signed reversal distance, part II 02 02 lit.: 2, permutations: π^2, π^3, hurdle, fortress
01.11.2018 – no class – – – –
08.10.2018 Signed reversal distance, part III; Sorting by reversals 02/03 03 lit.: 3, permutations: π^4, π^5, π^6
15.11.2018 Double-Cut-and-Join (DCJ) 04 04 lit.: 4
22.11.2018 DCJ with Insertions and Deletions 05 05 lit.: 5
29.11.2018 Genome Halving 06 06 lit.: 6, 7
06.12.2018 Guest lecture by F. Martinez: On the Gene Family-free DCJ Distance and Similarity slides – lit.: 8
13.12.2018 Algebraic Theory of Genome Rearrangements 07 07 lit.: 9
20.12.2018 Common Intervals of Permutations 08 08 lit.: 10, 11, 12
27.12.2018 – no class – – – –
03.01.2019 – no class – – – –
10.01.2019 Common Intervals of Strings 09, slides 09 lit.: 13, 14, 15
17.01.2019 Gene Teams – – lit.: 16, E. Demaine: Recurrences 1, 2
24.01.2019 Exam prep Q&A – – –
31.01.2019 Oral exam – – –

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