IMPROVED TOOLS FOR BIOLOGICAL SEQUENCE COMPARISON
IMPROVED TOOLS FOR BIOLOGICAL SEQUENCE COMPARISON
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DOI：
10.1073/pnas.85.8.2444
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发表时间：
1988-04-01
影响因子：
11.1
通讯作者：
LIPMAN, DJ
中科院分区：
文献类型：
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作者：
PEARSON, WR;LIPMAN, DJ
我们开发了三个用于比较蛋白质和DNA序列的计算机程序。它们可用于搜索序列数据库，评估相似性得分，并根据局部序列相似性缩进周期性结构。 FASTA程序是FASTP程序的更灵敏的导数，该程序可用于搜索蛋白质或DNA序列数据库，并可以通过搜索时翻译DNA数据库将蛋白质序列与DNA序列数据库进行比较。 FASTA在初始成对相似性分数的计算中包括一个额外的步骤，该步骤允许多个相似性的区域以增加相关序列的分数。 RDF2程序可用于使用保留局部序列组成的改组方法来评估相似性得分的重要性。使用相同的评分参数和相似的比对算法，LFASTA程序可以显示两个序列之间的所有局部相似性区域；这些局部相似性可以显示为“图形矩阵”图或单个比对。此外，这些程序已被推广，以允许根据各种替代评分矩阵比较DNA或蛋白质序列。
We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and indentify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.