Assignment of Orthologous Genes by Utilization of Multiple Databases - The Orthology Package in R

Steffen Priebe, Uwe Menzel

2013

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 highthroughput 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.

References

1. Zarse, K., Schmeisser, S., Groth, M., Priebe, S., Beuster, G., Kuhlow, D., Guthke, R., Platzer, M., Kahn, C. R., and Ristow, M. (2012). Impaired insulin/igf1 signaling extends life span by promoting mitochondrial l-proline catabolism to induce a transient ros signal. Cell Metab, 15(4):451-65.

Paper Citation

in Harvard Style

Priebe S. and Menzel U. (2013). Assignment of Orthologous Genes by Utilization of Multiple Databases - The Orthology Package in R . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 105-110. DOI: 10.5220/0004193201050110

in Bibtex Style

@conference{bioinformatics13,
author={Steffen Priebe and Uwe Menzel},
title={Assignment of Orthologous Genes by Utilization of Multiple Databases - The Orthology Package in R},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={105-110},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004193201050110},
isbn={978-989-8565-35-8},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - Assignment of Orthologous Genes by Utilization of Multiple Databases - The Orthology Package in R
SN - 978-989-8565-35-8
AU - Priebe S.
AU - Menzel U.
PY - 2013
SP - 105
EP - 110
DO - 10.5220/0004193201050110