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Eyüpoğlu, Can
Prof. Dr. Ismail SARITAS
Computer Science & IT

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Clustering of Mitochondrial D-loop Sequences Using Similarity Matrix, PCA and K-means Algorithm Eyüpoğlu, Can
International Journal of Intelligent Systems and Applications in Engineering 2016: Special Issue
Publisher : Prof. Dr. Ismail SARITAS

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18201/ijisae.2016Special Issue-146982

Abstract

In this study, mitochondrial displacement-loop (D-loop) sequences isolated from different hominid species are clustered using similarity matrix, Principal Component Analysis (PCA) and K-means algorithm. Firstly, the mitochondrial D-loop sequence data are retrieved from the GenBank database and copied into MATLAB. Pairwise distances are computed using p distance and Jukes-Cantor methods. A phylogenetic tree is created and then a similarity matrix is generated according to the pairwise distances. Furthermore, the clustering is performed using only K-means algorithm. After that PCA and K-means are used together in order to cluster mitochondrial D-loop sequences.
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