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Bioinformatics Vol. 17 no. 9 2001
Pages 853-854
© 2001 Oxford University Press

Applications Note

BioLayout—an automatic graph layout algorithm for similarity visualization

Anton J. Enright and Christos A. Ouzounis

Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK

Received on March 15, 2001 ; revised on June 29, 2001 ; accepted on July 2, 2001

Summary: Graph layout is extensively used in the field of mathematics and computer science, however these ideas and methods have not been extended in a general fashion to the construction of graphs for biological data. To this end, we have implemented a version of the Fruchterman Rheingold graph layout algorithm, extensively modified for the purpose of similarity analysis in biology. This algorithm rapidly and effectively generates clear two (2D) or three-dimensional (3D) graphs representing similarity relationships such as protein sequence similarity. The implementation of the algorithm is general and applicable to most types of similarity information for biological data.

Availability: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout

Contact: enright{at}ebi.ac.uk


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