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Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo‐amino acid composition

Recent advances in large‐scale genome sequencing have led to the rapid accumulation of amino acid sequences of proteins whose functions are unknown. Since the functions of these proteins are closely correlated with their subcellular localizations, many efforts have been made to develop a variety of methods for predicting protein subcellular location. In this study, based on the strategy by hybridizing the functional domain composition and the pseudo‐amino acid composition (Cai and Chou [ 2003 ]: Biochem. Biophys. Res. Commun. 305:407–411), the Intimate Sorting Algorithm (ISort predictor) was developed for predicting the protein subcellular location. As a showcase, the same plant and non‐plant protein datasets as investigated by the previous investigators were used for demonstration. The overall success rate by the jackknife test for the plant protein dataset was 85.4%, and that for the non‐plant protein dataset 91.9%. These are so far the highest success rates achieved for the two datasets by following a rigorous cross validation test procedure, further confirming that such a hybrid approach may become a very useful high‐throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. © 2004 Wiley‐Liss, Inc.