BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution

Fotis E Psomopoulos; Dimitrios M Vitsios; Shakuntala Baichoo; Christos A Ouzounis

doi:10.1093/bioinformatics/btw813

BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution

Bioinformatics. 2017 May 1;33(9):1418-1420. doi: 10.1093/bioinformatics/btw813.

Authors

Fotis E Psomopoulos¹, Dimitrios M Vitsios^{1

2}, Shakuntala Baichoo³, Christos A Ouzounis^{1

4}

Affiliations

¹ Computational Genomics Unit, Institute of Applied Biosciences, Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece.
² The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
³ Department of Computer Science & Engineering, Faculty of Engineering, University of Mauritius, Reduit 80837, Mauritius.
⁴ Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

PMID: 28453679
DOI: 10.1093/bioinformatics/btw813

Abstract

Summary: BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway. Thus, BioPAXViz can significantly facilitate, and contribute to, the study of metabolic pathway evolution and engineering.

Availability and implementation: BioPAXViz has been developed as a Cytoscape app and is available at: https://github.com/CGU-CERTH/BioPAX.Viz. The software is distributed under the MIT License and is accompanied by example files and data. Additional documentation is available at the aforementioned GitHub repository.

Contact: ouzounis@certh.gr.

MeSH terms

Computational Biology / methods*
Evolution, Molecular*
Metabolic Networks and Pathways / genetics*
Phylogeny
Software*