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Appl. Sci. 2016, 6(12), 406; doi:10.3390/app6120406

Numerical Characterization of Protein Sequences Based on the Generalized Chou’s Pseudo Amino Acid Composition

1,2,* , 1
and
2
1
Department of Mathematics, Bohai University, Jinzhou 121013, China
2
NIASRA—National Institute for Applied Statistics Research Australia, School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, Australia
*
Author to whom correspondence should be addressed.
Academic Editors: Yang Kuang and Wanbiao Ma
Received: 18 September 2016 / Revised: 30 October 2016 / Accepted: 29 November 2016 / Published: 6 December 2016
(This article belongs to the Special Issue Dynamical Models of Biology and Medicine)
View Full-Text   |   Download PDF [1148 KB, uploaded 6 December 2016]   |  

Abstract

The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical–chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a ( 21 + λ ) dimensional vector is constructed to characterize the protein sequence. The utility of the proposed approach is illustrated by phylogenetic analysis and identification of DNA-binding proteins. View Full-Text
Keywords: generalized pseudo amino acid composition; numerical characterization; phylogenetic analysis; identification of DNA-binding proteins generalized pseudo amino acid composition; numerical characterization; phylogenetic analysis; identification of DNA-binding proteins
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Li, C.; Li, X.; Lin, Y.-X. Numerical Characterization of Protein Sequences Based on the Generalized Chou’s Pseudo Amino Acid Composition. Appl. Sci. 2016, 6, 406.

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