Algorithms to detect multiprotein modularity conserved during evolution

Authors:
Luqman Hodgkinson;Richard M. Karp
Affiliations:
Computer Science Division, University of California, Berkeley, Center for Computational Biology, University of California, Berkeley, and the International Computer Science Institute;Computer Science Division, University of California, Berkeley, Center for Computational Biology, University of California, Berkeley, and the International Computer Science Institute
Venue:
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Year:
2011

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Abstract

Detecting essential multiprotein modules that change infrequently during evolution is a challenging algorithmic task that is important for understanding the structure, function, and evolution of the biological cell. In this paper, we present a linear-time algorithm, Produles, that improves on the running time of previous algorithms. We present a biologically motivated graph theoretic set of algorithm goals complementary to previous evaluation measures, demonstrate that Produles attains these goals more comprehensively than previous algorithms, and exhibit certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures.