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.

中文翻译：

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微生物视紫红质序列最佳比对的氨基酸取代基的构建和分析

氨基酸序列的成对比对是生物信息学的基本工具，它既可以独立使用，又可以在许多更复杂的方法中广泛使用。该工具的有效性在很大程度上取决于所使用的评分功能，该评分功能由替换矩阵和空位罚分组成。在这项工作中，构建并分析了微生物视紫红质（RHOD）超家族的氨基酸替代矩阵，然后将其与一组通用矩阵（BLOSUM，VTML，PFASUM）进行比较。结果表明，所有基质都可以构建几乎相同质量的微生物视紫红质序列，但只有BLOSUM和VTML基质及其与RHOD基质的线性组合才能显示出微生物视紫红质和直升机视紫红质之间的同源性。