DocumentCode :
139281
Title :
Construction of protein dendrograms based on amino acid indices and Discrete Fourier Transform
Author :
Chrysostomou, Charalambos ; Seker, Huseyin
Author_Institution :
Dept. of Genetics, Univ. of Leicester, Leicester, UK
fYear :
2014
fDate :
26-30 Aug. 2014
Firstpage :
816
Lastpage :
819
Abstract :
From the literature, existing methods use pairwise percent identity to identify the percentage of similarity between two protein sequences, in order to create a dendrogram. As this is a parametric method of measuring the similarities between proteins, and different parameter may yield different results, this method does not guarantee that the global optimal similarity values will be found. As protein dendrogram construction is used in other areas, such as multiple protein sequence alignments, it is very important that the most related protein sequences to be identified and align first. Furthermore, by using the pairwise percent identity of the protein sequences to construct the dendrograms, the physical characteristics of protein sequences and amino acids are not considered. In this paper, a new method was proposed for constructing protein sequence dendrograms. For this method, Discrete Fourier Transform, was used to construct the distance matrix in combination with the multiple amino acid indices that were used to encode protein sequences into numerical sequences. In order to show the applicability and robustness of the proposed method, a case study was presented by using nine Cluster of Differentiation 4 protein sequences extracted from the UniProt online database.
Keywords :
discrete Fourier transforms; molecular biophysics; organic compounds; proteins; UniProt online database; amino acid indices; differentiation cluster; discrete Fourier transform; distance matrix; multiple protein sequence alignments; pairwise percent identity; protein dendrogram construction; protein sequence dendrograms; Amino acids; Bioinformatics; Discrete Fourier transforms; Protein engineering; Protein sequence;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE
Conference_Location :
Chicago, IL
ISSN :
1557-170X
Type :
conf
DOI :
10.1109/EMBC.2014.6943716
Filename :
6943716
Link To Document :
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