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Algorithms in Comparative Genomics (2V + 2Ü)

392189 Dias Vieira Braga Winter 2020/21 Th 10:15 - 11:45 (V) online via Zoom
392192 Bohnenkämper Winter 2020/21 Fr 08:30 - 10:00 (Ü) online via Zoom

The details of both Zoom meetings were already announced via mail list.

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 and gene clusters.

Algorithms discussed in this course are mostly combinatorial by nature, similar to the sequence analysis course.

This lecture can ideally be combined with the seminar "Computational Pangenomics (2S)".

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

Literature

to be announced later

Topics

  1. Distance and Sorting
    • Breakpoint Distance
    • Double-Cut-and-Join (DCJ) distance
    • DCJ-indel distance
    • Reversal Distance
    • Single-Cut-or-Join (SCJ) distance
  2. Computing NP-hard distances via ILP
    • Balanced genomes
    • Natural genomes
    • Family-free genomes
  3. Ancestral Reconstruction
    • SCJ Median
    • Small Parsimony
  4. Common Intervals and Gene Clusters

Inversion Visualization Software

Prof. Istvan Miklos, from Alfréd Rényi Institute in Budapest, kindly shared his visualization software for the Breakpoint Diagram. 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, representing genome A (genome B is assumed to be the identity permutation), the numbers separated with a <tab>. There is an example in the provided archive.

Select the adjacency 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 Slides (S) S + notes Literature Exercises
29.10. Introduction, Genomes, Breakpoint distance S 1 SN 1 Tannier et al. 2009 Ex 1
05.11. Breakpoint and Single-Cut-or-Join (SCJ) distances S 2 SN 2 Feijão & Meidanis 2011 Ex 2
12.11. Breakpoint and SCJ median and halving S 3 SN 3 Ex 3
19.11. Breakpoint median/ Double-Cut-and-Join (DCJ) halving S 4 SN 4 Bryant 1998, Mixtacki 2008 Ex 4
26.11. DCJ distance and relational graph S 5 SN 5 Bergeron et al. 2006,
Kováč et al. 2011 		Ex 5
03.12. Inversion distance and relational diagram S 6 SN 6 Sorting by Reversals,
Hannenhalli and Pevzner 1999,
Bergeron et al. 2004		 Ex 6
10.12. Inversion distance / DCJ-indel distance S 7 SN 7 Braga et al. 2011 Ex 7
17.12. DCJ-indel distance / Restricted DCJ-indel distance S 8 SN 8 Braga and Stoye, 2015,
Braga et al. 2011b 		Ex 8 - Christmas
07.01. Capped relational graph S 9 SN 9 Bohnenkämper et al. 2020 Ex 9
14.01. DCJ with duplicated genes (double-distance / balanced genomes) S 10 SN 10 Tannier et al. 2009 Ex 10
21.01. ILP / DCJ distance of balanced genomes S 11 Shao et al. 2015
28.01. DCJ-indel distance of natural genomes Bohnenkämper et al. 2020
04.02. DCJ-indel distance of family-free genomes Rubert et al. 2020
11.02. t.b.a.