Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1109/TCBB.2018.2831661
Document accepted manuscript
Title (Primary) An exact algorithm for sorting by weighted preserving genome rearrangements
Author Hartmann, T.; Bernt, M. ORCID logo ; Middendorf, M.
Source Titel IEEE/ACM Transactions on Computational Biology and Bioinformatics
Year 2019
Department MOLSYB
Volume 16
Issue 1
Page From 52
Page To 62
Language englisch
Keywords Genome rearrangements; transposition; inversio; tandem duplication random loss; mitochondria; fungi; common interval

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.

Persistent UFZ Identifier
Hartmann, T., Bernt, M., Middendorf, M. (2019):
An exact algorithm for sorting by weighted preserving genome rearrangements
IEEE-ACM Trans. Comput. Biol. Bioinform. 16 (1), 52 - 62 10.1109/TCBB.2018.2831661