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Algorithms in Genome Research

392109/10 Stoye Winter 2020/21 Fr 9:00-10:30 and 10:30-12:00 in X-E1-200

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 Notes
30.10.2020 Introduction, logistics – –
06.11.2020 Physical mapping Exercises 1 –
13.11.2020 Genome assembly I Exercises 2 –
20.11.2020 Genome assembly II Exercises 3 –
27.11.2020 Genome annotation I Exercises 4 –
04.12.2020 Genome annotation II Exercises 5 Notes 5
11.12.2020 RNA sequencing Exercises 6 Notes 6
18.12.2020 Analysis of mass spectra Exercises 7 Notes 7
X-mas break
08.01.2021 SNV-disease association mapping Exercises 8 Notes 8
15.01.2021 Pangenomics Exercises 9 Notes 9
22.01.2021 Haplotype inference Exercises 10 Notes 10
29.01.2021 Comparative genomics I: Genome rearrangement Exercises 11 Notes 11
05.02.2021 Comparative genomics II: Gene cluster detection Exercises 12 Notes 12
12.02.2021 Metagenomics – Notes 13

Examination dates

Oral exams will be on 19 February 2021, either presential (if permitted) or online via Zoom. Please make an appointment with the secretary in U10-151, Heike Samuel.

A second oral exam can be taken in March 2021. Please contact Heike Samuel if you are interested.