Condensed Matrix Descriptor for Proteinb Sequence Comparison.

Abstract The present paper develops a novel way of reducing a protein sequence of any length to a real symmetric condensed 20 × 20 matrix. This condensed matrix can be nicely applied as a protein sequence descriptor. In fact, with such a condensed representation, comparison of two protein sequences...

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Bibliographic Details
Main Authors: S Pal, J Maji, Dilip B Bhattacharya, D K
Other Authors: The Pennsylvania State University CiteSeerX Archives
Format: Text
Language:English
Published: 2016
Subjects:
Blue whale
Fin whale
Online Access:http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1077.1838
http://file.scirp.org/pdf/IJAMSC_2016031713403020.pdf
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Summary:Abstract The present paper develops a novel way of reducing a protein sequence of any length to a real symmetric condensed 20 × 20 matrix. This condensed matrix can be nicely applied as a protein sequence descriptor. In fact, with such a condensed representation, comparison of two protein sequences is reduced to a comparison of two such 20 × 20 matrices. As each square matrix has a unique Alley Index/normalized Alley Index, such index is conveniently used in getting distance matrix to construct Phylogenetic trees of different protein sequences. Finally protein sequence comparison is made based on these Phylogenetic trees. In this paper three types viz., NADH dehydrogenase subunit 3 (ND3), subunit 4 (ND4) and subunit 5 (ND5) of protein sequences of nine species, Human, Gorilla, Common Chimpanzee, Pygmy Chimpanzee, Fin Whale, Blue Whale, Rat, Mouse and Opossum are used for comparison.

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