User Tools

Site Tools


teaching:2018summer:cg

Algorithms in Comparative Genomics (2V + 2Ü)

392189/92 Stoye Summer 2018 Fr 08:45 - 10:15 (Ü), Fr 10:15 - 11:45 (V) in U10-146 ekvv/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 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, the so-called Hannenhalli-Pevzner 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 English.

Conditions for participation, prior knowledge

Required: Algorithms and Data Structures (or comparable)
Recommended: Sequence Analysis and Foundations of Genome Research

Schedule

Date Topic Exercises Literature
13.04.2018 Organizational matters (just 10 minutes)
20.04.2018 – no class –
27.04.2018 Introduction
04.05.2018 Breakpoint Distance Exercises 1 Tannier et al. 2009
11.05.2018 Single Cut or Join Distance and Sorting Exercises 2 Feijão & Meidanis 2011
18.05.2018 – no class –
25.05.2018 Double Cut and Join Distance and Sorting Exercises 3 Bergeron et al. 2006
01.06.2018 Reversal Distance and Sorting Exercises 4 Bergeron et al. 2004
08.06.2018 The Genomic Distance and Sorting Exercises 5 Bergeron et al. 2009,
Erdős et al. 2011
15.06.2018 Double Cut and Join with Indels Exercises 6 Braga et al. 2011
22.06.2018 Multiple Genomes Exercises 7
(phylogenetic tree,
gene order data)
Feijão 2015
29.06.2018 Genome Halving Exercises 8 Mixtacki 2008
06.07.2018 Family-free Genome Comparison Exercises 9 Braga et al. 2013, Doerr et al. 2018
13.07.2018 – no class –
20.07.2018 Oral exams

Further oral exams can be scheduled on an individual basis.


Back to Teaching

teaching/2018summer/cg.txt · Last modified: 2018/09/11 13:41 by Jens Stoye