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首页> 外文期刊>Advances and Applications in Bioinformatics and Chemistry >Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST
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Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST

机译：通过BLAST和PSI-BLAST评估结构衍生的氨基酸替代基质在检测蛋白质同源物中的功效

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摘要

Abstract: The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blaST, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.
机译：摘要：全基因组测序项目产生的大量蛋白质序列需要快速准确的注释方法。通过计算序列分析检测同源性是确定蛋白质之间复杂的进化和功能关系的有力工具。同源搜索算法使用氨基酸取代矩阵来检测蛋白质序列之间的相似性。当今常用的取代基质是使用不参考蛋白质结构进行比对的序列构建的。在这里，我们介绍了根据蛋白质结构分类（SCOP）数据库中大量蛋白质结构域结构的比对构建的氨基酸取代矩阵。我们表明，当纳入同源搜索算法BLAST和PSI-blaST中时，基于结构的置换矩阵可增强检测远程同源物的功效。

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