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. 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. © The Author 2014.

GOssTo : a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology / H. Caniza, A.E. Romero, S. Heron, H. Yang, A. Devoto, M. Frasca, M. Mesiti, G. Valentini, A. Paccanaro. - In: BIOINFORMATICS. - ISSN 1367-4803. - 30:15(2014), pp. 2235-2236. [10.1093/bioinformatics/btu144]

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

M. Frasca;M. Mesiti;G. Valentini
Penultimo
;
2014

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. 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. © The Author 2014.
Settore INF/01 - Informatica
Settore ING-INF/05 - Sistemi di Elaborazione delle Informazioni
2014
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/238042
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