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

Chattopadhyay, Amit K., Nasiev, Diar and Flower, Darren R. (2015). A statistical physics perspective on alignment-independent protein sequence comparison. Bioinformatics, 31 (15), pp. 2469-2474.

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: Engineering & Applied Sciences > Mathematics
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Life & Health Sciences > Pharmacy
Life & Health Sciences
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
Full Text Link: http://bioinformatics.oxfordjournals.org/content/31/15/2469
Related URLs: http://www.scopus.com/inward/record.url?scp=84943633576&partnerID=8YFLogxK (Scopus URL)
Published Date: 2015
Authors: Chattopadhyay, Amit K.
Nasiev, Diar
Flower, Darren R. ( 0000-0002-8542-7067)

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