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Algorithms in Genome Research


392109/10 Pedro Feijão Fr 8:45-10:15/Fr 10:15-11:45 in T2-208 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
10.10.2014 Introduction, logistics / Genome rearrangements - Reversals 1 Slides Exercises
17.10.2014 Genome rearrangements - Reversals 2 Slides
24.10.2014 (no class) —
31.10.2014 Genome annotation I: Introduction to HMMs Exercises ExerciseList2.zip Solve 1,2(b), 3(b)
07.11.2014 Genome annotation II: Finding protein-coding genes —
14.11.2014 Reversals without Hurdles and Fortresses Slides Exercises
21.11.2014 Genome rearrangements - DCJ operation Slides Exercises
28.11.2014 Physical mapping PQ-tree (University of Washington) Exercises
05.12.2014 Sequence assembly I Lecture notes by Daniel Huson Exercises
12.12.2014 Sequence assembly II Main Reference Exercises
19.12.2014 Sequence assembly III Comparative genome assembly Exercises
09.01.2015 RNA sequencing I - EST and RNA-Seq Assembly Ref 1 Ref 2 Exercises
16.01.2015 RNA sequencing II - Microarrays Ref 1 Exercises
23.01.2015 Gene Clusters Ref 1 Exercises
30.01.2015 Gene Clusters II Reference Exercises
06.02.2015 Metagenomics –

Examination dates

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