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Algorithms in Genome Research


392109/10 Pedro Feijão, Jens Stoye Fr 8:45-10:15/Fr 10:15-11:45 in U10-146 ekvv (V) ekvv (Ü)

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.

Software

Reversals and BP Graph

Prof. Istvan Miklos, from the Bioinformatics Group in Alfréd Rényi Institute in Budapest, kindly shared his visualization software for the Breakpoint Graph. It is written in Java, and you can download it here.

Usage: java InversionVisualisation file_name

For example: java InversionVisualisation permutation.txt

The input must be a signed permutation in one line, the numbers separated with a TAB. There are some examples in the package.

Select the black 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.

Time table:

Date Topic Exercises
23.10.2015 Introduction, logistics (Pedro, Jens) –
30.10.2015 Genome Assembly I (Jens) Exercises 1
06.11.2015 (no class) –
13.11.2015 Genome Assembly II (Jens) Exercises 2
20.11.2015 Transcriptomics, RNA-Seq (Jens) Exercises 3
27.11.2015 RNomics (Pedro) Exercises 4
04.12.2015 Mass Spectrometry for Proteomics and Metabolomics (Jens) Exercises 5
11.12.2015 Computational Systems Biology (Jens) Exercises 6
18.12.2015 Genome Annotation (Jens) Exercises 7
08.01.2016 Sorting By Reversals I (Pedro) Exercises 8
15.01.2016 Sorting By Reversals II (Pedro) Exercises 9
22.01.2016 Sorting by DCJ (Pedro) Exercises 10
29.01.2016 Reconstruction of Ancestral Genomes (Pedro) Exercises 11
05.02.2016 Haplotype Inference (Pedro) Exercises 12
12.02.2016 Metagenomics, Astrobiology (Pedro) –

Examination dates

Oral exams will be on 26.02.2016. Please make an appointment with the secretary in U10-151, Heike Samuel.

If necessary, a second oral exam can be scheduled on an individual basis until end of March 2016.

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