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Bioinformatics. 2014 Aug 1;30(15):2235-6. doi: 10.1093/bioinformatics/btu144. Epub 2014 Mar 22.

GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.

Author information

1
Department of Computer Science, Royal Holloway, University of London, Egham, TW200EX, UK, School of Mathematics, Statistics & Applied Mathematics, National University of Ireland, Galway, School of Biological Sciences, Royal Holloway, University of London, Egham, TW200EX, UK and Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.

Abstract

SUMMARY:

We present GOssTo, the Gene Ontology semantic similarity Tool, a user-friendly software system for calculating semantic similarities between gene products according to the Gene Ontology. GOssTo is bundled with six semantic similarity measures, including both term- and graph-based measures, and has extension capabilities to allow the user to add new similarities. Importantly, for any measure, GOssTo can also calculate the Random Walk Contribution that has been shown to greatly improve the accuracy of similarity measures. GOssTo is very fast, easy to use, and it allows the calculation of similarities on a genomic scale in a few minutes on a regular desktop machine.

CONTACT:

alberto@cs.rhul.ac.uk

AVAILABILITY:

GOssTo is available both as a stand-alone application running on GNU/Linux, Windows and MacOS from www.paccanarolab.org/gossto and as a web application from www.paccanarolab.org/gosstoweb. The stand-alone application features a simple and concise command line interface for easy integration into high-throughput data processing pipelines.

PMID:
24659104
PMCID:
PMC4103586
DOI:
10.1093/bioinformatics/btu144
[Indexed for MEDLINE]
Free PMC Article
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