A statistical physics perspective on alignment-independent protein sequence comparison.

Abstract

Motivation: Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function, and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Results: Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from “first passage probability distribution” to summarize statistics of ensemble averaged amino acid propensity values. In this paper, we introduce and elaborate this approach.

Publication DOI: https://doi.org/10.1093/bioinformatics/btv167
Divisions: College of Engineering & Physical Sciences > School of Informatics and Digital Engineering > Mathematics
College of Engineering & Physical Sciences > Systems analytics research institute (SARI)
College of Health & Life Sciences > Aston Pharmacy School
College of Health & Life Sciences
College of Health & Life Sciences > Chronic and Communicable Conditions
Additional Information: © The Author(s) 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Funding: Work supported by Aston University.
Uncontrolled Keywords: Biochemistry,Molecular Biology,Computational Theory and Mathematics,Computer Science Applications,Computational Mathematics,Statistics and Probability
Publication ISSN: 1367-4803
Full Text Link:
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
http://bioinfor ... tent/31/15/2469 (Publisher URL)
PURE Output Type: Article
Published Date: 2015-08-01
Published Online Date: 2015-03-25
Authors: Chattopadhyay, Amit K. (ORCID Profile 0000-0001-5499-6008)
Nasiev, Diar
Flower, Darren R. (ORCID Profile 0000-0002-8542-7067)

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License: Creative Commons Attribution


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