DOI: 10.1142/s0219720006001771. DETECTING AND SORTING TARGETING PEPTIDES WITH NEURAL NETWORKS AND SUPPORT VECTOR MACHINES

DETECTING AND SORTING TARGETING PEPTIDES WITH NEURAL NETWORKS AND SUPPORT VECTOR MACHINES

10.1142/s0219720006001771

Crossref journal-article

World Scientific Pub Co Pte Ltd

Journal of Bioinformatics and Computational Biology (219)

Abstract

This paper presents a composite multi-layer classifier system for predicting the subcellular localization of proteins based on their amino acid sequence. The work is an extension of our previous predictor PProwler v1.1 which is itself built upon the series of predictors SignalP and TargetP. In this study we outline experiments conducted to improve the classifier design. The major improvement came from using Support Vector machines as a "smart gate" sorting the outputs of several different targeting peptide detection networks. Our final model (PProwler v1.2) gives MCC values of 0.873 for non-plant and 0.849 for plant proteins. The model improves upon the accuracy of our previous subcellular localization predictor (PProwler v1.1) by 2% for plant data (which represents 7.5% improvement upon TargetP).

Bibliography

HAWKINS, J., & BODÃN, M. (2006). DETECTING AND SORTING TARGETING PEPTIDES WITH NEURAL NETWORKS AND SUPPORT VECTOR MACHINES. Journal of Bioinformatics and Computational Biology, 04(01), 1â18.

Authors 2

JOHN HAWKINS (first)
MIKAEL BODÉN (additional)

References 19 Referenced 55

10.1093/bioinformatics/16.5.412
10.1093/bioinformatics/15.11.937
{'key': 'rf4', 'volume': '16', 'author': 'Bodén M.', 'journal-title': 'IEEE Transactions on Neural Networks'} / IEEE Transactions on Neural Networks by Bodén M.
10.1093/bioinformatics/bti372
10.1073/pnas.97.1.262
{'key': 'rf7', 'first-page': '195', 'volume': '7', 'author': 'Elman J. L.', 'journal-title': 'Machine Learning'} / Machine Learning by Elman J. L.
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{'key': 'rf13', 'first-page': '227', 'volume': '7', 'author': 'Pollack J. B.', 'journal-title': 'Machine Learning'} / Machine Learning by Pollack J. B.
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{'key': 'rf18', 'volume-title': 'Statistical Learning Theory', 'author': 'Vapnik V.', 'year': '1998'} / Statistical Learning Theory by Vapnik V. (1998)
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{'key': 'rf20', 'volume-title': 'Data Mining: Practical Machine Learning Tools with Java Implementations', 'author': 'Witten I. H.', 'year': '2000'} / Data Mining: Practical Machine Learning Tools with Java Implementations by Witten I. H. (2000)

Dates

Type	When
Created	19 years, 5 months ago (March 27, 2006, 7:43 p.m.)
Deposited	1 year, 7 months ago (Feb. 3, 2024, 8:37 a.m.)
Indexed	1 month, 1 week ago (July 25, 2025, 6:42 a.m.)
Issued	19 years, 7 months ago (Feb. 1, 2006)
Published	19 years, 7 months ago (Feb. 1, 2006)
Published Online	13 years, 9 months ago (Nov. 21, 2011)
Published Print	19 years, 7 months ago (Feb. 1, 2006)

Funders 0

None

BibTeX

@article{HAWKINS_2006, title={DETECTING AND SORTING TARGETING PEPTIDES WITH NEURAL NETWORKS AND SUPPORT VECTOR MACHINES}, volume={04}, ISSN={1757-6334}, url={http://dx.doi.org/10.1142/s0219720006001771}, DOI={10.1142/s0219720006001771}, number={01}, journal={Journal of Bioinformatics and Computational Biology}, publisher={World Scientific Pub Co Pte Ltd}, author={HAWKINS, JOHN and BODÉN, MIKAEL}, year={2006}, month=feb, pages={1–18} }

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