NDLI: Construction of protein distance matrix based on amino acid indices and Discrete Fourier Transform

Content Provider	IEEE Xplore Digital Library
Author	Chrysostomou, C. Seker, H.
Copyright Year	2013
Description	Author affiliation: Dept. of Genetics, Univ. of Leicester, Leicester, UK (Chrysostomou, C.) \|\| Bio-Health Inf. Res. Group, De Montfort Univ., Leicester, UK (Seker, H.)
Abstract	Protein distance matrix is widely used in various protein sequence analyses, and mainly obtained by using pairwise sequence alignment scores or protein sequence homology, which fail to take into consideration of individual physical characteristics of protein sequences and amino acids, or a combination of these features. In this paper, a new method is therefore proposed for constructing protein distance matrix based on natural amino acid indices in combination with Discrete Fourier Transform (DFT). For the proposed method, protein distance matrices can be generated using any given set of amino acid indices, each one of which represents a unique biological feature of protein sequences. In this study, the results are based on the combination of 25 widely accepted amino acid indices, which produced the best results, according to the biological relationships between proteins. As a case study 26 Cluster of Differentiation 4 (CD4) protein sequences were used in order to construct a distance matrix based on the proposed method. The results show that the pairwise relationship between CD4 protein sequences remain the same in comparison with their pairwise percent identity. For another group of protein sequences the pairwise relationship between CD4 protein sequences dramatically changed with the proposed method in comparison to the pairwise percent identity. The proposed distance matrix has been shown to have a positive impact on these case studies and therefore is expected to be useful in several fields such as multiple protein sequence alignment and phylogenetic analysis, where an accurate distance matrix based on natural generalized protein properties plays an important role.
Starting Page	4066
Ending Page	4069
File Size	229367
Page Count	4
File Format	PDF
ISBN	9781457702167
ISSN	1557170X
DOI	10.1109/EMBC.2013.6610438
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-07-03
Publisher Place	Japan
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Amino acids Protein engineering Discrete Fourier transforms Protein sequence Indexes Protein Sequences Amino Acid Indices Cluster of Differentiation 4 (CD4) Distance Matrix Discrete Fourier Transform (DFT)
Content Type	Text
Resource Type	Article
Subject	Signal Processing Biomedical Engineering Health Informatics Computer Vision and Pattern Recognition

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