Title: Automatic 2D hydrophobic cluster alignment

Authors: Phisit Kannasut, Rath Pichyangkura, Chotirat Ann Ratanamahatana

Addresses: Department of Computer Engineering, Chulalongkorn University, Bangkok, Thailand. ' Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand. ' Department of Computer Engineering, Chulalongkorn University, Bangkok, Thailand

Abstract: Biological databases in the past decade have tremendously grown in size. However, effective retrieval data is still a great challenge. In particular, we need a high-quality tool to measure similarity among protein sequences within the database instead of 1D alignment software. In this work, we implement a 2D visualisation tool for amino acid and propose a new protein representation that could be used effectively in our 2D automatic Hydrophobic Cluster Alignment software. The resulting evolution trees and the alignment results from the PIR database have demonstrated that homologous proteins with the same functionalities obtain high sequence identity score.

Keywords: bioinformatics; HCA; hydrophobic cluster analysis; protein homology; automatic alignment; similarity measures; cluster alignment; visualisation; amino acids; protein representation; protein sequences.

DOI: 10.1504/IJBET.2010.029651

International Journal of Biomedical Engineering and Technology, 2010 Vol.3 No.1/2, pp.43 - 63

Published online: 30 Nov 2009 *

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