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Sequence-based prediction of protein-protein interactions by means of codon usage

Hamed Shateri Najafabadi12 and Reza Salavati123*

Author Affiliations

1 Institute of Parasitology, McGill University, Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec H9X 3V9, Canada

2 McGill Centre for Bioinformatics, McGill University, University Street, Montreal, Quebec H3A 2B4, Canada

3 Department of Biochemistry, McGill University, Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada

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Genome Biology 2008, 9:R87  doi:10.1186/gb-2008-9-5-r87

Published: 23 May 2008


We introduce a novel approach to predict interaction of two proteins solely by analyzing their coding sequences. We found that similarity in codon usage is a strong predictor of protein-protein interactions and, for high specificity values, is as sensitive as the most powerful current prediction methods. Furthermore, combining codon usage with other predictors results in a 75% increase in sensitivity at a precision of 50%, compared to prediction without considering codon usage.