Algorithms for the Analysis of Approximate Gene Cluster (3AGC)

This project is realized in cooperation with the AG Genome Informatics of Prof. Dr. Jens Stoye at Bielefeld University, Germany. The order of genes in genomes can be used to determine the function of unknown genes, as well as the phylogenetic history of the organisms. In view of the ever-increasing speed of genome sequencing, there exists a huge amount of data for such studies. On the algorithmic side, though, methods are often based on overly simplified genome models, use heuristics to solve optimization problems, or suffer from long running times. Gene clusters are sets of genes that occur as single contiguous blocks in several genomes. Unfortunately, the requirement of exact occurrences of gene clusters turns out to be too strict for the biological application. In this project, we are developing models and algorithms for the computation of approximate gene clusters, that combine a formal strictness with applicability to biological data. At the same time, our algorithms must be swift to allow application to the increasing amount of genome data. We are combining methods from combinatorial optimization and algorithmic graph theory with a statistically sound evaluation.

Antragsteller Sebastian Böcker
Lehrstuhl Lehrstuhl Bioinformatik
Drittmittelgeber DFG - Deutsche Forschungsgemeinschaft
Laufzeit Januar 2010 - Februar 2014
Stellen 2
Besetzung Martin Engler
Sascha Winter
Projektart Einzelprojekt
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