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DNA Research Advance Access published online on June 15, 2007
DNA Research, doi:10.1093/dnares/dsm011
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© The Author 2007. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Proteome-Wide Prediction of Novel DNA/RNA-Binding Proteins Using Amino Acid Composition and Periodicity in the Hyperthermophilic Archaeon Pyrococcus furiosus

Kosuke Fujishima1,2, Mizuki Komasa1,2, Sayaka Kitamura1,2, Haruo Suzuki1,2, Masaru Tomita1,3 and Akio Kanai1,3,*

1 Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
2 Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-8520, Japan
3 Faculty of Environment and Information Studies, Keio University, Fujisawa 252-8520, Japan

Received 13 March 2007 ; revised 30 April 2007

Proteins play a critical role in complex biological systems, yet about half of the proteins in publicly available databases are annotated as functionally unknown. Proteome-wide functional classification using bioinformatics approaches thus is becoming an important method for revealing unknown protein functions. Using the hyperthermophilic archaeon Pyrococcus furiosus as a model species, we used the support vector machine (SVM) method to discriminate DNA/RNA-binding proteins from proteins with other functions, using amino acid composition and periodicities as feature vectors. We defined this value as the composition score (CO) and periodicity score (PD). The P. furiosus proteins were classified into three classes (I–III) on the basis of the two-dimensional correlation analysis of CO score and PD score. As a result, approximately 87% of the functionally known proteins categorized as class I proteins (CO score + PD score > 0.6) were found to be DNA/RNA-binding proteins. Applying the two-dimensional correlation analysis to the 994 hypothetical proteins in P. furiosus, a total of 151 proteins were predicted to be novel DNA/RNA-binding protein candidates. DNA/RNA-binding activities of randomly chosen hypothetical proteins were experimentally verified. Six out of seven candidate proteins in class I possessed DNA/RNA-binding activities, supporting the efficacy of our method.

Key words: DNA/RNA-binding protein; amino acid periodicity; support vector machine; archaea

* To whom correspondence should be addressed. Tel. +81 235-29-0524. Fax. +81 235-29-0525. E-mail: akio{at}sfc.keio.ac.jp

Communicated by Takashi Ito.


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