Numerical Characterization of Protein Sequences and Application to Voltage-Gated Sodium Channel α Subunit Phylogeny

Article type: Research Article

Authors: Nandy, Ashesh | Ghosh, Ambarnil | Nandy, Papiya

Affiliations: School of Environmental Studies, Jadavpur University, Kolkata 700032, India | Physics Department, Jadavpur University, Kolkata 700032, India

Note: [] Corresponding author. E-mail: [email protected]

Abstract: We propose a new method to compare sequences of protein families by generating numerical characterizations through a 20D representation. Using a walk along the axes representing the amino acids we generate a vector for each sequence whose components can be used to derive distance matrices between sequences and whose magnitudes can be used to compare the similarities/dissimilarities between the different sequences. The distance matrices enable creation of phylogenetic trees without need for multiple alignments or any other model dependencies. In this paper we test this technique with human globin gene sequences and then apply the method to a contemporary issue of evolutionary relationships of rat and human voltage-gated sodium channel α subunits and compare with published literature. The close match of the results demonstrates the reliability and ease of use of this method.

Keywords: Protein distance matrix, 20D graphical representation, phylogenetic tree, voltage-gated sodium channels, evolution

DOI: 10.3233/ISB-2009-0389

Journal: In Silico Biology, vol. 9, no. 3, pp. 77-87, 2009