Algorithms in Genome Research

392109/10 Stoye Winter 2021/22 Fr 9:00-10:30 and 10:30-12:00 in U10-146

Contents

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.

Literature

The page AlgGRLiterature contains many links to the original literature.

Time table

Date Topic Exercises
15.10.2021 no class
22.10.2021 Introduction, logistics
29.10.2021 no class
05.11.2021 Physical mapping/consecutive ones problem Exercises 1
12.11.2021 Genome assembly I Exercises 2
19.11.2021 Genome assembly II Exercises 3
26.11.2021 Genome annotation Exercises 4
03.12.2021 no class
10.12.2021 Sequence alignment Exercises 5
17.12.2021 Transcriptomics (RNA sequencing) Exercises 6
X-mas break
07.01.2022 (XXL) RNA secondary structure prediction, analysis of mass spectra Exercises 7/8
14.01.2022 Haplotype inference Exercises 9
21.01.2022 SNP-disease association mapping Exercises 10
28.01.2022 Computational pangenomics Exercises 11
04.02.2022 Computational metagenomics

Examination dates

Oral exams (in presence) will be on 18 February 2022. Please make an appointment with the secretary in U10-151, Heike Samuel.

A second oral exam can be taken in March 2022. Please contact Heike Samuel if you are interested.