, Volume 52, Issue 2, pp 114-132
Date: 22 Sep 2007

Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection

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Color-coding is a technique to design fixed-parameter algorithms for several NP-complete subgraph isomorphism problems. Somewhat surprisingly, not much work has so far been spent on the actual implementation of algorithms that are based on color-coding, despite the elegance of this technique and its wide range of applicability to practically important problems. This work gives various novel algorithmic improvements for color-coding, both from a worst-case perspective as well as under practical considerations. We apply the resulting implementation to the identification of signaling pathways in protein interaction networks, demonstrating that our improvements speed up the color-coding algorithm by orders of magnitude over previous implementations. This allows more complex and larger structures to be identified in reasonable time; many biologically relevant instances can even be solved in seconds where, previously, hours were required.

An extended abstract of this paper appeared under the title “Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection” in the Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007), January 15–17, 2007, Hong Kong, China, volume 5 in Advances in Bioinformatics and Computational Biology, pages 277–286, Imperial College Press.
F. Hüffner supported by the Deutsche Forschungsgemeinschaft, Emmy Noether research group PIAF (fixed-parameter algorithms), NI 369/4.
S. Wernicke supported by the Deutsche Telekom Stiftung.
T. Zichner supported by the Deutsche Forschungsgemeinschaft, project PEAL (Parameterized Complexity and Exact Algorithms), NI 369/1 and OPAL (Optimal Solutions for Hard Problems in Computational Biology), NI 369/2.