Sequence analysis is the primary and simplest approach to discover structural, functional and evolutionary details of related proteins. All the alignment based approaches of sequence analysis make use of amino acid substitution matrices, and the accuracy of the results largely depends on the type of scoring matrices used to perform alignment tasks. An amino acid substitution matrix is a 20 × 20 matrix in which the individual elements encapsulate the rates at which each of the 20 amino acid residues in proteins are substituted by other amino acid residues over time. In contrast to most globular/ordered proteins whose amino acids composition is considered as standard, there are several classes of proteins (e.g., transmembrane proteins) in which certain types of amino acid (e.g., hydrophobic residues) are enriched. These compositional differences among various classes of proteins are manifested in their underlying residue substitution frequencies. Therefore, each of the compositionally distinct class of proteins or protein segments should be studied using specific scoring matrices that reflect their distinct residue substitution pattern. In this review, we describe the development and application of various substitution scoring matrices peculiar to proteins with standard and biased compositions. Along with most commonly used standard matrices (PAM, BLOSUM, MD and VTML) that act as default parameters in various homologs search and alignment tools, different substitution scoring matrices specific to compositionally distinct class of proteins are discussed in detail.

中文翻译：

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蛋白质的替代评分矩阵 - 概述。

序列分析是发现相关蛋白质的结构、功能和进化细节的主要和最简单的方法。所有基于比对的序列分析方法都使用氨基酸替代矩阵，结果的准确性在很大程度上取决于用于执行比对任务的评分矩阵的类型。氨基酸置换矩阵是一个 20 × 20 矩阵，其中各个元素封装了蛋白质中 20 个氨基酸残基中的每个氨基酸残基随时间被其他氨基酸残基置换的速率。与将氨基酸组成视为标准的大多数球状/有序蛋白质相比，有几类蛋白质（例如跨膜蛋白）富含某些类型的氨基酸（例如疏水残基）。各类蛋白质之间的这些组成差异体现在它们潜在的残基替换频率上。因此，应使用反映其不同残基替换模式的特定评分矩阵来研究每个组成不同类别的蛋白质或蛋白质片段。在这篇综述中，我们描述了具有标准和偏向成分的蛋白质特有的各种替代评分矩阵的开发和应用。除了在各种同源搜索和比对工具中充当默认参数的最常用的标准矩阵（PAM、BLOSUM、MD 和 VTML）外，还详细讨论了特定于组成不同类别的蛋白质的不同替代评分矩阵。