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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2012

Open Access Open Badges Research

A subgraph isomorphism algorithm and its application to biochemical data

Vincenzo Bonnici1, Rosalba Giugno2*, Alfredo Pulvirenti2, Dennis Shasha3 and Alfredo Ferro2

Author Affiliations

1 Dept. Computer Science - University of Verona, Verona, 37134, Italy

2 Dept. Clinical and Molecular Biomedicine - University of Catania, Catania, 95125, Italy

3 Courant Institute of Mathematical Sciences - New York University, NY 10012, USA

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BMC Bioinformatics 2013, 14(Suppl 7):S13  doi:10.1186/1471-2105-14-S7-S13

Published: 22 April 2013



Graphs can represent biological networks at the molecular, protein, or species level. An important query is to find all matches of a pattern graph to a target graph. Accomplishing this is inherently difficult (NP-complete) and the efficiency of heuristic algorithms for the problem may depend upon the input graphs. The common aim of existing algorithms is to eliminate unsuccessful mappings as early as and as inexpensively as possible.


We propose a new subgraph isomorphism algorithm which applies a search strategy to significantly reduce the search space without using any complex pruning rules or domain reduction procedures. We compare our method with the most recent and efficient subgraph isomorphism algorithms (VFlib, LAD, and our C++ implementation of FocusSearch which was originally distributed in Modula2) on synthetic, molecules, and interaction networks data. We show a significant reduction in the running time of our approach compared with these other excellent methods and show that our algorithm scales well as memory demands increase.


Subgraph isomorphism algorithms are intensively used by biochemical tools. Our analysis gives a comprehensive comparison of different software approaches to subgraph isomorphism highlighting their weaknesses and strengths. This will help researchers make a rational choice among methods depending on their application. We also distribute an open-source package including our system and our own C++ implementation of FocusSearch together with all the used datasets ( webcite). In future work, our findings may be extended to approximate subgraph isomorphism algorithms.

Subgraph isomorphism algorithms; biochemical graph data; search strategies; algorithms comparisons and distributions