A Cytoscape app for motif enumeration with ISMAGS

Thomas Van Parys; Ine Melckenbeeck; Maarten Houbraken; Pieter Audenaert; Didier Colle; Mario Pickavet; Piet Demeester; Yves Van de Peer

doi:10.1093/bioinformatics/btw626

A Cytoscape app for motif enumeration with ISMAGS

Bioinformatics. 2017 Feb 1;33(3):461-463. doi: 10.1093/bioinformatics/btw626.

Authors

Thomas Van Parys^{1

2

3}, Ine Melckenbeeck⁴, Maarten Houbraken⁴, Pieter Audenaert^{3

4}, Didier Colle^{3

4}, Mario Pickavet^{3

4}, Piet Demeester^{3

4}, Yves Van de Peer^{1

2

3

5}

Affiliations

¹ Department of Plant Systems Biology, VIB, Ghent, Belgium.
² Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
³ Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
⁴ Department of Information Technology (INTEC), Ghent University - iMinds, Ghent, Belgium.
⁵ Genomics Research Institute, University of Pretoria, Pretoria, South Africa.

PMID: 28158465
DOI: 10.1093/bioinformatics/btw626

Abstract

Summary: We present a Cytoscape app for the ISMAGS algorithm, which can enumerate all instances of a motif in a graph, making optimal use of the motif’s symmetries to make the search more efficient. The Cytoscape app provides a handy interface for this algorithm, which allows more efficient network analysis.

Availability and implementation: The Cytoscape app for ISMAGS can be freely downloaded from the Cytoscape App store http://apps.cytoscape.org/apps/ismags. Source code and documentation for ISMAGS are available at https://github.com/biointec/ismags. Source code and documentation for the Cytoscape app are available at https://gitlab.psb.ugent.be/thpar/ISMAGS_Cytoscape.

Contacts: Pieter.Audenaert@intec.ugent.be or Yves.VanDePeer@psb.vib-ugent.be

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Algorithms
Computational Biology / methods*
Computer Graphics
Software*