Back to Search
Start Over
On the consistency of orthology relationships.
- Source :
-
BMC Bioinformatics . 2016 Suppl 14, Vol. 17, p251-262. 12p. 6 Diagrams, 1 Chart, 1 Graph. - Publication Year :
- 2016
-
Abstract
- Background: Orthologs inference is the starting point of most comparative genomics studies and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/paralogy relationships C on a collection of n genes. Results: We give the first polynomial algorithm-more precisely a O(n3) time algorithm-to decide whether C is consistent, even when the species tree is unknown. We also investigate a biologically meaningful optimization version of these problems, in which we wish to minimize the number of duplication events; unfortunately, we show that all these optimization problems are NP-hard and are unlikely to have good polynomial time approximation algorithms. Conclusions: Our polynomial algorithm for checking consistency has been implemented in Python and is available. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 17
- Database :
- Academic Search Index
- Journal :
- BMC Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 127994128
- Full Text :
- https://doi.org/10.1186/s12859-016-1267-3