Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

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Abstract

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.

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Details

Original languageEnglish
Pages (from-to)1720-1730
Number of pages11
JournalJournal of Biomolecular Structure and Dynamics
Volume33
Issue8
Early online date28 Oct 2014
DOIs
StatePublished - 2015

Bibliographic note

Supplementary material: http://dx.doi.10.1080/07391102.2014.968624

Keywords

  • Chou’s pseudo amino acid composition, DNA-binding proteins, evolutionary information, top-n-gram-SVM

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