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An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical representation

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A new two-dimensional graphical representation of protein sequences is introduced. Twenty concentric evenly spaced circles divided by n radial lines into equal divisions are selected to represent any protein sequence of length n. Each circle represents one of the different 20 amino acids, and each radial line represents a single amino acid of the protein sequence. An efficient numerical method based on the graph is proposed to measure the similarity between two protein sequences. To prove the accuracy of our approach, the method is applied to NADH dehydrogenase subunit 5 (ND5) proteins of nine different species and 24 transferrin sequences from vertebrates. High values of correlation coefficient between our results and the results of ClustalW are obtained (approximately perfect correlations). These values are higher than the values obtained in many other related works.
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Keywords: correlation and significance analysis; graphical representation; mathematical descriptors; protein sequences; similarity analysis

Document Type: Research Article

Affiliations: Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt

Publication date: February 1, 2015

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