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Genome Biol. 2008;9(5):R87. doi: 10.1186/gb-2008-9-5-r87. Epub 2008 May 23.

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

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


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.

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