Title: A software tool for protein sequence alignment

Authors: Justin Lee; Shawn X. Wang

Addresses: Raytheon, El Segundo, CA 90245, USA ' Department of Computer Science, California State University, Fullerton, CA 92831, USA

Abstract: Protein sequence comparison is one of the most popular techniques for protein data analysis. Because a specific function of a protein is often determined by a small segment in the sequence, algorithms for optimal local alignment are among the most studied. In this paper, we introduce an effective tool called information specific algorithm (INSPAL) that is not based on any specific cost model, instead allowing the user to adjust the parameters for alignment according to the sequences under consideration and the biological properties that are specific to these sequences. Experimental comparison with two most popular alignment tools ALIGN and SIM indicated that INSPAL generated better alignment results with appropriate settings of the parameters. INSPAL was developed as a Windows Installer Package using Microsoft Visual Studio C++ 6.0. It provides a user friendly graphic user interface and is very easy to install and use.

Keywords: protein sequence alignment; hydrophobicity; Pascarella Value; dynamic algorithm; bioinformatics.

DOI: 10.1504/IJBRA.2020.113018

International Journal of Bioinformatics Research and Applications, 2020 Vol.16 No.4, pp.319 - 335

Received: 08 Dec 2017
Accepted: 03 Feb 2018
Published online: 16 Feb 2021 *

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