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SLiMScape: a protein short linear motif analysis plugin for Cytoscape

Kevin T O’Brien123, Niall J Haslam123 and Denis C Shields123*

Author Affiliations

1 UCD Conway, Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland

2 UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland

3 School of Medicine and Medical Science, University College Dublin, Dublin, Ireland

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BMC Bioinformatics 2013, 14:224  doi:10.1186/1471-2105-14-224

Published: 15 July 2013

Abstract

Background

Computational protein short linear motif discovery can use protein interaction information to search for motifs among proteins which share a common interactor. Cytoscape provides a visual interface for protein networks but there is no streamlined way to rapidly visualize motifs in a network of proteins, or to integrate computational discovery with such visualizations.

Results

We present SLiMScape, a Cytoscape plugin, which enables both de novo motif discovery and searches for instances of known motifs. Data is presented using Cytoscape’s visualization features thus providing an intuitive interface for interpreting results. The distribution of discovered or user-defined motifs may be selectively displayed and the distribution of protein domains may be viewed simultaneously. To facilitate this SLiMScape automatically retrieves domains for each protein.

Conclusion

SLiMScape provides a platform for performing short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment. This significantly aids in the discovery of novel short linear motifs and in visualizing the distribution of known motifs.