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Amino Acids. 2008 Jan;34(1):103-9. Epub 2007 Jul 12.

Predicting DNA-binding proteins: approached from Chou's pseudo amino acid composition and other specific sequence features.

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College of Chemistry, Sichuan University, Chengdu, China.


DNA-binding proteins play a pivotal role in gene regulation. It is vitally important to develop an automated and efficient method for timely identification of novel DNA-binding proteins. In this study, we proposed a method based on alone the primary sequences of proteins to predict the DNA-binding proteins. DNA-binding proteins were encoded by autocross-covariance transform, pseudo-amino acid composition, dipeptide composition, respectively and also the different combinations of the three encoded methods; further, these feature matrices were applied to support vector machine classifiers to predict the DNA-binding proteins. All modules were trained and validated by the jackknife cross-validation test. Through comparing the performance of these substituted modules, the best result was obtained from pseudo-amino acid composition with the overall accuracy of 96.6% and the sensitivity of 90.7%. The results suggest that it can efficiently predict the novel DNA-binding proteins only using the primary sequences.

[Indexed for MEDLINE]

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