Loading…

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

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....

Full description

Saved in:
Bibliographic Details
Published in:Moscow University biological sciences bulletin 2019, Vol.74 (1), p.21-25
Main Authors: Novoseletsky, V. N., Armeev, G. A., Shaitan, K. V.
Format: Article
Language:English
Subjects:
Citations: Items that this one cites
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0096-3925
1934-791X
DOI:10.3103/S009639251901005X