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This article is part of the supplement: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

Open Access Open Badges Research

Classification of protein sequences by means of irredundant patterns

Matteo Comin* and Davide Verzotto

Author Affiliations

Department of Information Engineering, University of Padova, Italy

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BMC Bioinformatics 2010, 11(Suppl 1):S16  doi:10.1186/1471-2105-11-S1-S16

Published: 18 January 2010



The classification of protein sequences using string algorithms provides valuable insights for protein function prediction. Several methods, based on a variety of different patterns, have been previously proposed. Almost all string-based approaches discover patterns that are not "independent, " and therefore the associated scores overcount, a multiple number of times, the contribution of patterns that cover the same region of a sequence.


In this paper we use a class of patterns, called irredundant, that is specifically designed to address this issue. Loosely speaking the set of irredundant patterns is the smallest class of "independent" patterns that can describe all common patterns in two sequences, thus they avoid overcounting. We present a novel discriminative method, called Irredundant Class, based on the statistics of irredundant patterns combined with the power of support vector machines.


Tests on benchmark data show that Irredundant Class outperforms most of the string algorithms previously proposed, and it achieves results as good as current state-of-the-art methods. Moreover the footprints of the most discriminative irredundant patterns can be used to guide the identification of functional regions in protein sequences.