Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(4) © Oxford University Press 2004; all rights reserved.
Predicting subcellular localization of proteins using machine-learned classifiers
Department of Computing Science, University of Alberta, Edmonton, AB, Canada, T6G 2E8
Received on August 26, 2003
; accepted on September 25, 2003
Advance Access Publication January 22, 2004
Motivation: Identifying the destination or localization of proteins is key to understanding their function and facilitating their purification. A number of existing computational prediction methods are based on sequence analysis. However, these methods are limited in scope, accuracy and most particularly breadth of coverage. Rather than using sequence information alone, we have explored the use of database text annotations from homologs and machine learning to substantially improve the prediction of subcellular location.
Results: We have constructed five machine-learning classifiers for predicting subcellular localization of proteins from animals, plants, fungi, Gram-negative bacteria and Gram-positive bacteria, which are 81% accurate for fungi and 92–94% accurate for the other four categories. These are the most accurate subcellular predictors across the widest set of organisms ever published. Our predictors are part of the Proteome Analyst web-service.
Availability: http://www.cs.ualberta.ca/~bioinfo/PA/Sub, http://www.cs.ualberta.ca/~bioinfo/PA
Supplementary information: http://www.cs.ualberta.ca/~bioinfo/PA/Subcellular
Contact: bioinfo{at}cs.ualberta.ca
* To whom correspondence should be addressed.
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