Information de reference pour ce titreAccession Number: | 00124336-200503010-00008.
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Author: | Gardy, J. L. 1; Laird, M. R. 1; Chen, F. 2; Rey, S. 1; Walsh, C. J. 1; Ester, M. 2; Brinkman, F. S. L. 1,*
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Institution: | (1)Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6 (2)Department of Computing Science, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
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Title: | PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.[Miscellaneous]
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Source: | Bioinformatics. 21(5):617-623, March 1, 2005.
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Abstract: | 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 are as follows: 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 was 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.
(C) Copyright Oxford University Press 2005.
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References: | Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
Chung, Y.S., Breidt, F., Dubnau, D. (1998) Cell surface localization and processing of the ComG proteins, required for DNA binding during transformation of Bacillus subtilis. Mol. Microbiol., 29, 905-913.
Gardy, J.L., Spencer, C., Wang, K., Ester, M., Tusnady, G.E., Simon, I., Hua, S., deFays, K., Lambert, C., Nakai, K., Brinkman, F.S.L. (2003) PSORTb: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res., 31, 3613-3617.
Hua, S. and Sun, Z. (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics, 17, 721-728.
Hulo, N., Sigrist, C.J.A., Le Saux, V., Langendijk-Genevaux, P.S., Bordoli, L., Gattiker, A., De Castro, E., Bucher, P., Bairoch, A. (2004) Recent improvements to the PROSITE database. Nucleic Acids Res., 32, D134-D137.
Joachims, T. (2002) SVMLight.
Lin, C. (2003) LibSVM.
Lu, Z., Szafron, D., Greiner, R., Lu, P., Wishart, D.S., Poulin, B., Anvik, J., Macdonell, C., Eisner, R. (2004) Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics, 20, 547-556.
Nakai, K. and Kanehisa, M. (1991) Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins, 11, 95-110.
Nielsen, H., Engelbrecht, J., Brunak, S., von Heijne, G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
Schneider, G. and Fechner, U. (2004) Advances in the prediction of protein targeting signals. Proteomics, 4, 1571-1580.
She, R., Chen, F., Wang, K., Ester, M., Gardy, J.L., Brinkman, F.S.L. (2003) Frequent-subsequence-based prediction of outer membrane proteins. Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, NY ACM Press, pp. 436-445.
Tusnady, G.E. and Simon, I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
Vapnik, V. The Nature of Statistical Learning Theory (1995), NY Springer.
Wang, J.T., Chirn, G., Marr, T.G., Shapiro, B., Shasha, D., Zhang, K. (1994) Combinatorial pattern discovery for scientific data: some preliminary results. Proceedings of the 1994 ACM SIGMOD International Conference on Management of Data, NY ACM Press, pp. 115-125.
Yu, C., Lin, C., Hwang, J. (2004) Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci., 13, 1402-1406.
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Language: | English.
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Document Type: | Sequence analysis.
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Journal Subset: | Life Sciences.
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ISSN: | 1367-4803
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NLM Journal Code: | cw9, 9808944
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