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

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 fr...

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Bibliographic Details
Published in:Network biology 2019-12, Vol.9 (4), p.78-95
Main Author: Mathur, Rinku
Format: Article
Language:English
Subjects:
Alignment
Deoxyribonucleic acid
DNA
dna sequences
euclidean distance
Euclidean geometry
fuzzy linear programming
Gene sequencing
Linear programming
Nucleotide sequence
Nucleotides
phylogenetic network
Phylogenetics
Phylogeny
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Summary: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.
ISSN:2220-8879
2220-8879