Abstract:
The preserving Genome Sorting Problem (pGSP) asks for a shortest sequence of rearrangement operations that transforms a given gene order into another given gene order by ...Show MoreMetadata
Abstract:
The preserving Genome Sorting Problem (pGSP) asks for a shortest sequence of rearrangement operations that transforms a given gene order into another given gene order by using rearrangement operations that preserve common intervals, i.e., groups of genes that form an interval in both given gene orders. The wpGSP is the weighted version of the problem were each type of rearrangement operation has a weight and a minimum weight sequence of rearrangement operations is sought. An exact algorithm - called CREx2 - is presented, which solves the wpGSP for arbitrary gene orders and the following types of rearrangement operations: inversions, transpositions, inverse transpositions, and tandem duplication random loss operations. CREx2 has a (worst case) exponential runtime, but a linear runtime for problem instances where the common intervals are organized in a linear structure. The efficiency of CREx2 and its usefulness for phylogenetic analysis is shown empirically for gene orders of fungal mitochondrial genomes.
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics ( Volume: 16, Issue: 1, 01 Jan.-Feb. 2019)
Funding Agency:
Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, Germany
Tom Hartmann received the diploma degree in mathematics with biology as minor and optimization as specialty, in 2014. Currently, he is working toward the PhD degree in the Faculty of Mathematics and Computer Science, University of Leipzig, where he is associated with the Swarm Intelligence and Complex Systems Group. His research interests include are bioinformatics, design of algorithms for cophylogenetics, swarm intellig...Show More
Tom Hartmann received the diploma degree in mathematics with biology as minor and optimization as specialty, in 2014. Currently, he is working toward the PhD degree in the Faculty of Mathematics and Computer Science, University of Leipzig, where he is associated with the Swarm Intelligence and Complex Systems Group. His research interests include are bioinformatics, design of algorithms for cophylogenetics, swarm intellig...View more
Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, Leipzig, Germany
Matthias Bernt received the diploma and Dr rer nat degrees from the University of Leipzig, in 2004 and 2010, respectively. After postdocs with the Algorithms and Computational Biology Laboratory, National Taiwan University, Taipei and the Swarm Intelligence and Complex Systems Group, University of Leipzig, Germany, he is now responsible for the bioinformatics support at the Helmholtz Centre for Environmental Research-UFZ....Show More
Matthias Bernt received the diploma and Dr rer nat degrees from the University of Leipzig, in 2004 and 2010, respectively. After postdocs with the Algorithms and Computational Biology Laboratory, National Taiwan University, Taipei and the Swarm Intelligence and Complex Systems Group, University of Leipzig, Germany, he is now responsible for the bioinformatics support at the Helmholtz Centre for Environmental Research-UFZ....View more
Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, Germany
Martin Middendorf received the diploma degree in mathematics and the Dr rer nat degree from the University of Hannover, Germany, in 1988 and 1992, respectively, and the Professoral Habilitation degree from the University of Karlsruhe, Germany, in 1998. He has worked with the University of Dortmund, Germany, and the University of Hannover as a visiting professor of computer science. He was a professor of computer science w...Show More
Martin Middendorf received the diploma degree in mathematics and the Dr rer nat degree from the University of Hannover, Germany, in 1988 and 1992, respectively, and the Professoral Habilitation degree from the University of Karlsruhe, Germany, in 1998. He has worked with the University of Dortmund, Germany, and the University of Hannover as a visiting professor of computer science. He was a professor of computer science w...View more
Contents Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, Germany
Tom Hartmann received the diploma degree in mathematics with biology as minor and optimization as specialty, in 2014. Currently, he is working toward the PhD degree in the Faculty of Mathematics and Computer Science, University of Leipzig, where he is associated with the Swarm Intelligence and Complex Systems Group. His research interests include are bioinformatics, design of algorithms for cophylogenetics, swarm intelligence, and genome rearrangements.
Tom Hartmann received the diploma degree in mathematics with biology as minor and optimization as specialty, in 2014. Currently, he is working toward the PhD degree in the Faculty of Mathematics and Computer Science, University of Leipzig, where he is associated with the Swarm Intelligence and Complex Systems Group. His research interests include are bioinformatics, design of algorithms for cophylogenetics, swarm intelligence, and genome rearrangements.View more
Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, Leipzig, Germany
Matthias Bernt received the diploma and Dr rer nat degrees from the University of Leipzig, in 2004 and 2010, respectively. After postdocs with the Algorithms and Computational Biology Laboratory, National Taiwan University, Taipei and the Swarm Intelligence and Complex Systems Group, University of Leipzig, Germany, he is now responsible for the bioinformatics support at the Helmholtz Centre for Environmental Research-UFZ. His research interests include bioinformatics, combinatorial optimization problems, and mitochondrial genetics.
Matthias Bernt received the diploma and Dr rer nat degrees from the University of Leipzig, in 2004 and 2010, respectively. After postdocs with the Algorithms and Computational Biology Laboratory, National Taiwan University, Taipei and the Swarm Intelligence and Complex Systems Group, University of Leipzig, Germany, he is now responsible for the bioinformatics support at the Helmholtz Centre for Environmental Research-UFZ. His research interests include bioinformatics, combinatorial optimization problems, and mitochondrial genetics.View more
Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, Germany
Martin Middendorf received the diploma degree in mathematics and the Dr rer nat degree from the University of Hannover, Germany, in 1988 and 1992, respectively, and the Professoral Habilitation degree from the University of Karlsruhe, Germany, in 1998. He has worked with the University of Dortmund, Germany, and the University of Hannover as a visiting professor of computer science. He was a professor of computer science with the Catholic University of Eichstätt, Germany. He is currently a professor of the Swarm Intelligence and Complex Systems Group, University of Leipzig, Germany. His research interests include algorithms from nature, bioinformatics, and swarm intelligence.
Martin Middendorf received the diploma degree in mathematics and the Dr rer nat degree from the University of Hannover, Germany, in 1988 and 1992, respectively, and the Professoral Habilitation degree from the University of Karlsruhe, Germany, in 1998. He has worked with the University of Dortmund, Germany, and the University of Hannover as a visiting professor of computer science. He was a professor of computer science with the Catholic University of Eichstätt, Germany. He is currently a professor of the Swarm Intelligence and Complex Systems Group, University of Leipzig, Germany. His research interests include algorithms from nature, bioinformatics, and swarm intelligence.View more
