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Construction and Analysis of Amino Acid Substitution Matrices for Optimal Alignment of Microbial Rhodopsin Sequences

Construction and Analysis of Amino Acid Substitution Matrices for Optimal Alignment of Microbial... Pairwise alignment of amino acid sequences is the basic tool of bioinformatics, which is widely used both independently and within numerous more complex methods. The effectiveness of this tool critically depends on the scoring function used, which consists of a substitution matrix and gap penalties. In this work, amino acid substitution matrices for the superfamily of microbial rhodopsins (RHOD) were constructed and analyzed and then compared with a set of general-purpose matrices (BLOSUM, VTML, PFASUM). It was shown that all matrices allow constructing alignments of microbial rhodopsin sequences of almost the same quality, but only BLOSUM and VTML matrices and their linear combinations with RHOD matrices allow revealing homology between microbial rhodopsins and heliorhodopsin. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Moscow University Biological Sciences Bulletin Springer Journals

Construction and Analysis of Amino Acid Substitution Matrices for Optimal Alignment of Microbial Rhodopsin Sequences

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References (24)

Publisher
Springer Journals
Copyright
Copyright © 2019 by Allerton Press, Inc.
Subject
Life Sciences; Biochemistry, general; Cell Biology; Life Sciences, general; Plant Sciences; Zoology
ISSN
0096-3925
eISSN
1934-791X
DOI
10.3103/S009639251901005X
Publisher site
See Article on Publisher Site

Abstract

Pairwise alignment of amino acid sequences is the basic tool of bioinformatics, which is widely used both independently and within numerous more complex methods. The effectiveness of this tool critically depends on the scoring function used, which consists of a substitution matrix and gap penalties. In this work, amino acid substitution matrices for the superfamily of microbial rhodopsins (RHOD) were constructed and analyzed and then compared with a set of general-purpose matrices (BLOSUM, VTML, PFASUM). It was shown that all matrices allow constructing alignments of microbial rhodopsin sequences of almost the same quality, but only BLOSUM and VTML matrices and their linear combinations with RHOD matrices allow revealing homology between microbial rhodopsins and heliorhodopsin.

Journal

Moscow University Biological Sciences BulletinSpringer Journals

Published: May 24, 2019

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