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Authors: Steffen Priebe 1 and Uwe Menzel 2

Affiliations: 1 Hans-Knöll-Institute, Germany ; 2 Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Germany

ISBN: 978-989-8565-35-8

Keyword(s): Orthologs, Databases, Multi-species, R Programming Language.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Databases and Data Management ; Soft Computing ; Visualization

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 connec ted 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. (More)

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Paper citation in several formats:
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

@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},
}

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

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