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BioMed Research International
Volume 2013, Article ID 263829, 7 pages
http://dx.doi.org/10.1155/2013/263829
Research Article

SubMito-PSPCP: Predicting Protein Submitochondrial Locations by Hybridizing Positional Specific Physicochemical Properties with Pseudoamino Acid Compositions

Pufeng Du1,2 and Yuan Yu1,2

1School of Computer Science and Technology, Tianjin University, Tianjin 300072, China
2Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin 300072, China

Received 12 May 2013; Revised 10 July 2013; Accepted 20 July 2013

Academic Editor: Lei Chen

Copyright © 2013 Pufeng Du and Yuan Yu. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Knowing the submitochondrial location of a mitochondrial protein is an important step in understanding its function. We developed a new method for predicting protein submitochondrial locations by introducing a new concept: positional specific physicochemical properties. With the framework of general form pseudoamino acid compositions, our method used only about 100 features to represent protein sequences, which is much simpler than the existing methods. On the dataset of SubMito, our method achieved over 93% overall accuracy, with 98.60% for inner membrane, 93.90% for matrix, and 70.70% for outer membrane, which are comparable to all state-of-the-art methods. As our method can be used as a general method to upgrade all pseudoamino-acid-composition-based methods, it should be very useful in future studies. We implement our method as an online service: SubMito-PSPCP.