Bioinformatics Advance Access published online on October 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti057
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
* To whom correspondence should be addressed.
Motivation: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work were: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria, and then carry out a comparative analysis of localization. Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines were introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size. Availability: Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. Supplementary Information: http://www.psort.org/psortb/supplementaryinfo.html.
Revised September 17, 2004
Accepted September 28, 2004
Article
PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
2 Department of Computing Science, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
F. S. L. Brinkman, E-mail: brinkman{at}sfu.ca
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J. S. Paddick, S. R. Brailsford, S. Rao, R. F. Soares, E. A. M. Kidd, D. Beighton, and K. A. Homer Effect of Biofilm Growth on Expression of Surface Proteins of Actinomyces naeslundii Genospecies 2. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3774 - 3779. [Abstract] [Full Text] [PDF]
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B.-C. Kim, X. Qian, C. Leang, M. V. Coppi, and D. R. Lovley Two Putative c-Type Multiheme Cytochromes Required for the Expression of OmcB, an Outer Membrane Protein Essential for Optimal Fe(III) Reduction in Geobacter sulfurreducens. J. Bacteriol., April 1, 2006; 188(8): 3138 - 3142. [Abstract] [Full Text] [PDF]
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A. Mooney, N. D. O'Leary, and A. D. W. Dobson Cloning and Functional Characterization of the styE Gene, Involved in Styrene Transport in Pseudomonas putida CA-3 Appl. Envir. Microbiol., February 1, 2006; 72(2): 1302 - 1309. [Abstract] [Full Text] [PDF]
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M. R. Couturier, E. Tasca, C. Montecucco, and M. Stein Interaction with CagF Is Required for Translocation of CagA into the Host via the Helicobacter pylori Type IV Secretion System Infect. Immun., January 1, 2006; 74(1): 273 - 281. [Abstract] [Full Text] [PDF]
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J. D. Glasner, M. Rusch, P. Liss, G. Plunkett III, E. L. Cabot, A. Darling, B. D. Anderson, P. Infield-Harm, M. C. Gilson, and N. T. Perna ASAP: a resource for annotating, curating, comparing, and disseminating genomic data Nucleic Acids Res., January 1, 2006; 34(suppl_1): D41 - D45. [Abstract] [Full Text] [PDF]
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D. Xie, A. Li, M. Wang, Z. Fan, and H. Feng LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST Nucleic Acids Res., July 1, 2005; 33(suppl_2): W105 - W110. [Abstract] [Full Text] [PDF]
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