A Cytoscape app for motif enumeration with ISMAGS

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Authors

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

Journal Title

Journal ISSN

Volume Title

Publisher

Oxford University Press

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.

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Keywords

Cytoscape app, Network motifs, Motifs in protein, ISMAGS

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Citation

Van Parys, T, Melckenbeeck, I, Houbraken, M, Audenaert, P, Colle, D, Pickavet, M, Demeester, P & Van de Peer, Y 2017, 'A Cytoscape app for motif enumeration with ISMAGS, Bioinformatics, vol. 33, no. 3, pp. 461-463.