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A new measure of dissimilarity and fuzzy linear programming model to construct phylogenetic network among DNA sequences

Authors :
Rinku Mathur
Neeru Adlakha
Source :
Network Biology, Vol 9, Iss 4, Pp 78-95 (2019)
Publication Year :
2019
Publisher :
International Academy of Ecology and Environmental Sciences, 2019.

Abstract

The growth of DNA databases used to store large number of biological sequence data, has stimulated the importance of alignment of sequences for phylogenetics. Most of the phylogenetic methods based on alignment of sequences consume long time to provide the results. In this regard, a new alignment free measure, based on frequency of occurrence of different nucleotides in sequences has been reported. The Euclidean distance metric has been used over these frequencies of nucleotides to obtain the dissimilarities among DNA sequences. These distances are then used to construct the phylogenetic tree among sequences. In addition, a fuzzy linear programming model has been developed here to construct the phylogenetic network which is considered as the generalized form of phylogenetic tree. As an application, the proposed method is applied over the data set of beta - globin gene of nine species and is validated by comparing the obtained results with the already existing method. The results obtained are more promising over the available method and can be applied over any length of input data sequences.

Details

Language :
English
ISSN :
22208879
Volume :
9
Issue :
4
Database :
Directory of Open Access Journals
Journal :
Network Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.30e8542ed3ec4174a0821a2ad7b373e9
Document Type :
article