Algorithms in Genome Research

392109/10 Jens Stoye Fr 10:15-11:45/Fr 8:45-10:15 in U10-146 ekvv/ekvv


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.


The page AlgGRLiterature contains many links to the original literature.

Time table:

Date Topic Exercises
14.10.2011 Introduction, logistics (none)
21.10.2011 (no class)
28.10.2011 (no class)
04.11.2011 De-novo HTS genome assembly Number 1
11.11.2011 Comparative HTS genome assembly Number 2
18.11.2011 RNA and protein-coding gene finding Number 3
25.11.2011 Finding patterns in non-coding regions Number 4
02.12.2011 RNA-seq Number 5
09.12.2011 Analysis of mass spectra ( Example ) Number 6
16.12.2011 Genome rearrangement Number 7
23.12.2011 Genome halving Number 8
30.12.2011 — christmas break —
06.01.2012 — christmas break —
13.01.2012 Gene clusters Number 9
20.01.2012 Reconstruction of ancestral genomes (by Roland Wittler) Number 10 \\ phylogenetic tree
gene order data
27.01.2012 Haplotype inference and SNP-disease association mining Number 11
03.02.2012 Metagenomics and astrobiology

Organisational Matters:

Together with the practical course “Bioinformatics Applications in Genome Research” in the following summer semester, this lecture forms the master module Algorithms in Genome Research.
The exercises will not be corrected or graded, but presence and activity during the exercise hours is expected. Credit points will be given based on an oral exam at the end of the semester.


Mündliche Prüfung Mo 27.02.2012 ganztägig
Mündliche Prüfung Di 28.02.2012 ganztägig