Phylogenetic analysis of some leguminous trees using CLUSTALW2 bioinformatics tool

Sagar Patel, H. Panchal, K. Anjaria
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引用次数: 13

Abstract

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally for Protein. MSA has wide range of applications and to cite few of them such as phylogenetic analysis, protein pattern identification, protein domain identification, prediction of protein structure, structural similarity of amino acids and to get evolutionary similarity. ClustalW2 is a general purpose global multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. The output from ClustalW2 shows the best match for the selected sequences and lines up them in such a way that the identities, similarities and differences can be easily understood. Evolutionary relationships can be seen by creating Cladograms or Phylograms. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. In this paper, protein sequences of few legume species from UNIPROT database were taken and focused on MSA for protein sequences for these tree species of family Leguminosae, where ClustalW2 tool have used to generate biological data. The results are discussed with the help of Cladograms and Phylograms for selected tree species.
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利用CLUSTALW2生物信息学工具分析豆科树木的系统发育
多序列比对(multiple sequence alignment, MSA)是对三个或更多生物序列的比对,通常用于蛋白质。MSA具有广泛的应用,在系统发育分析、蛋白质模式鉴定、蛋白质结构域鉴定、蛋白质结构预测、氨基酸结构相似性以及获得进化相似性等方面都有广泛的应用。ClustalW2是一个通用的蛋白质全局多序列比对程序。它产生具有生物学意义的不同序列的多序列比对。ClustalW2的输出显示了所选序列的最佳匹配,并以一种易于理解的同一性、相似性和差异性的方式将它们排列起来。进化关系可以通过创建枝状图或系统图来观察。首先,对部分比对的序列赋予单独的权值,降低近重复序列的权值,提高差异最大的序列的权值;其次,在不同的比对阶段,氨基酸取代矩阵根据待比对序列的差异而变化。第三,残基特异性间隙惩罚和亲水区域局部减少的间隙惩罚鼓励潜在环区域产生新的间隙,而不是规则的二级结构。第四,在已经打开缺口的早期队列中的位置,当地会减少缺口处罚,以鼓励在这些位置上打开新的缺口。本文选取UNIPROT数据库中少数豆科植物的蛋白质序列,利用ClustalW2工具对这些豆科植物的蛋白质序列进行MSA分析。通过对所选树种的枝状图和系统图进行了讨论。
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