DOI: 10.1110/ps.051597405. A novel representation of protein sequences for prediction of subcellular location using support vector machines

A novel representation of protein sequences for prediction of subcellular location using support vector machines

10.1110/ps.051597405

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractAs the number of complete genomes rapidly increases, accurate methods to automatically predict the subcellular location of proteins are increasingly useful to help their functional annotation. In order to improve the predictive accuracy of the many prediction methods developed to date, a novel representation of protein sequences is proposed. This representation involves local compositions of amino acids and twin amino acids, and local frequencies of distance between successive (basic, hydrophobic, and other) amino acids. For calculating the local features, each sequence is split into three parts: N‐terminal, middle, and C‐terminal. The N‐terminal part is further divided into four regions to consider ambiguity in the length and position of signal sequences. We tested this representation with support vector machines on two data sets extracted from the SWISS‐PROT database. Through fivefold cross‐validation tests, overall accuracies of more than 87% and 91% were obtained for eukaryotic and prokaryotic proteins, respectively. It is concluded that considering the respective features in the N‐terminal, middle, and C‐terminal parts is helpful to predict the subcellular location.

Bibliography

Matsuda, S., Vert, J., Saigo, H., Ueda, N., Toh, H., & Akutsu, T. (2005). A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Science, 14(11), 2804â2813. Portico.

Authors 6

Setsuro Matsuda (first)
Jean‐Philippe Vert (additional)
Hiroto Saigo (additional)
Nobuhisa Ueda (additional)
Hiroyuki Toh (additional)
Tatsuya Akutsu (additional)

References 43 Referenced 123

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Dates

Type	When
Created	19 years, 9 months ago (Oct. 26, 2005, 2:02 p.m.)
Deposited	1 year, 10 months ago (Oct. 9, 2023, 4:16 p.m.)
Indexed	11 months, 3 weeks ago (Aug. 27, 2024, 8:33 p.m.)
Issued	19 years, 9 months ago (Nov. 1, 2005)
Published	19 years, 9 months ago (Nov. 1, 2005)
Published Online	16 years, 7 months ago (Jan. 1, 2009)
Published Print	19 years, 9 months ago (Nov. 1, 2005)

Funders 0

None

BibTeX

@article{Matsuda_2005, title={A novel representation of protein sequences for prediction of subcellular location using support vector machines}, volume={14}, ISSN={1469-896X}, url={http://dx.doi.org/10.1110/ps.051597405}, DOI={10.1110/ps.051597405}, number={11}, journal={Protein Science}, publisher={Wiley}, author={Matsuda, Setsuro and Vert, Jean‐Philippe and Saigo, Hiroto and Ueda, Nobuhisa and Toh, Hiroyuki and Akutsu, Tatsuya}, year={2005}, month=nov, pages={2804–2813} }

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