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Open Access Highly Accessed Research article

TESTLoc: protein subcellular localization prediction from EST data

Yao-Qing Shen* and Gertraud Burger

Author Affiliations

Robert-Cedergren Center for Bioinformatics and Genomics; Biochemistry Department, Université de Montréal, 2900 Edouard-Montpetit, Montreal, QC, H3T 1J4, Canada

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BMC Bioinformatics 2010, 11:563  doi:10.1186/1471-2105-11-563

Published: 15 November 2010

Abstract

Background

The eukaryotic cell has an intricate architecture with compartments and substructures dedicated to particular biological processes. Knowing the subcellular location of proteins not only indicates how bio-processes are organized in different cellular compartments, but also contributes to unravelling the function of individual proteins. Computational localization prediction is possible based on sequence information alone, and has been successfully applied to proteins from virtually all subcellular compartments and all domains of life. However, we realized that current prediction tools do not perform well on partial protein sequences such as those inferred from Expressed Sequence Tag (EST) data, limiting the exploitation of the large and taxonomically most comprehensive body of sequence information from eukaryotes.

Results

We developed a new predictor, TESTLoc, suited for subcellular localization prediction of proteins based on their partial sequence conceptually translated from ESTs (EST-peptides). Support Vector Machine (SVM) is used as computational method and EST-peptides are represented by different features such as amino acid composition and physicochemical properties. When TESTLoc was applied to the most challenging test case (plant data), it yielded high accuracy (~85%).

Conclusions

TESTLoc is a localization prediction tool tailored for EST data. It provides a variety of models for the users to choose from, and is available for download at http://megasun.bch.umontreal.ca/~shenyq/TESTLoc/TESTLoc.html webcite