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

被引：0
作者：
Novoseletsky V.N. [1 ]
Armeev G.A. [1 ]
Shaitan K.V. [1 ]
机构：
[1] Department of Biology, Moscow State University, Moscow
来源：
Moscow University Biological Sciences Bulletin | 2019年 / 74卷 / 1期
基金：
俄罗斯基础研究基金会;
关键词：
entropy; heliorhodopsin; homology search; microbial rhodopsins; sequence alignment; substitution matrix;
D O I：
10.3103/S009639251901005X
中图分类号：
学科分类号：
摘要：
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. © 2019, Allerton Press, Inc.
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页码：21 / 25
页数：4
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