Assignment of orthologous genes by utilization of multiple databases: the orthology package in R

Priebe S, Menzel U (2013) Assignment of orthologous genes by utilization of multiple databases: the orthology package in R In: Pedro Fernandes, Jordi Solé-Casals, Ana Fred and Hugo Gamboa (eds.) Bioinformatics 2013 - 4th Int. Conf. on Bioinformatics Models, Methods and Algorithms 1. International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona /Spain, 02/11/2013-02/14/2013, pp. 105-110.SCITEPRESS – Science and Technology Publications, Lissabon /Portugal. ISBN: 978-989-8565358.

Abstract

 The assignment of orthologous genes between species is a key issue when multiple-species approaches are
conducted.  This has become even more relevant over the past years, triggered by the development of high-
throughput genome sequencing technologies, which enable access to complete genomes in a rapid and cost-
effective way. In this paper, we present a new software that allows the user to access orthology relationships
across multiple species in an easy, fast, and flexible manner. The tool collects data from three prominent freely
available databases, and presents it to the user in a convenient, easily accessible way.  Once the package is
installed, the software works on the local computer, therewith circumventing runtime delay caused by network
traffic often being a critical performance bottleneck when large datasets are studied or many organisms are
investigated simultaneously. By the consequent internal usage of unique identifiers, the software disburdens
the user from problems connected with the existence of synonyms or ambiguous gene denotations, a problem
that often hampers a clear-cut assignment of orthologs. The software is able to display frequently occurring,
complicated many-to-many orthology relationships in a visual manner.  It is written in the R programming
language and freely available.

Leibniz-HKI-Authors

Uwe Menzel
Steffen Priebe