Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
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DOI：
10.1093/nar/gkh610
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发表时间：
2004-05-01
影响因子：
14.9
通讯作者：
Lee, B
中科院分区：
文献类型：
--
作者：
Goonesekere, NCW;Lee, B
空位罚分是在搜索同源蛋白质和蛋白质序列的精确比对时所需的评分方案的重要组成部分。大多数同源性搜索和序列比对算法采用启发式“仿射空位罚分”方案q + r × n，其中q是打开空位的罚分，r是延伸空位的罚分，n是空位差距长度。为了设计一个更合理的评分方案，我们研究了在结构对齐的蛋白质结构域对的数据库中出现的缺口的模式。我们发现，间隙的频率的对数随差距的长度线性变化，但在间隙的长度为3处有一个中断，并且可以很好地近似于R-2值为1.0和0.99的两条线性回归线。当空位通过差距侧翼的两个残基的二级结构分类时，双线性行为被保留。当使用另一个完全独立的结构对齐的蛋白质对数据库时，得到了类似的结果。这些结果表明仿射空位罚函数的修改。
Gap penalty is an important component of the scoring scheme that is needed when searching for homologous proteins and for accurate alignment of protein sequences. Most homology search and sequence alignment algorithms employ a heuristic 'affine gap penalty' scheme q + r x n, in which q is the penalty for opening a gap, r the penalty for extending it and n the gap length. In order to devise a more rational scoring scheme, we examined the pattern of gaps that occur in a database of structurally aligned protein domain pairs. We find that the logarithm of the frequency of gaps varies linearly with the length of the gap, but with a break at a gap of length 3, and is well approximated by two linear regression lines with R-2 values of 1.0 and 0.99. The bilinear behavior is retained when gaps are categorized by secondary structures of the two residues flanking the gap. Similar results were obtained when another, totally independent, structurally aligned protein pair database was used. These results suggest a modification of the affine gap penalty function.