THE SIZE DISTRIBUTION OF INSERTIONS AND DELETIONS IN HUMAN AND RODENT PSEUDOGENES SUGGESTS THE LOGARITHMIC GAP PENALTY FOR SEQUENCE ALIGNMENT
THE SIZE DISTRIBUTION OF INSERTIONS AND DELETIONS IN HUMAN AND RODENT PSEUDOGENES SUGGESTS THE LOGARITHMIC GAP PENALTY FOR SEQUENCE ALIGNMENT
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DOI：
10.1007/bf00164032
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发表时间：
1995-04-01
影响因子：
3.9
通讯作者：
LI, WH
中科院分区：
文献类型：
--
作者：
GU, X;LI, WH
缺失、插入和插入缺失的大小分布（即，插入或缺失）进行了研究。结果表明：（1）在序列进化中，缺失比插入发生得更频繁，没有一个假基因的插入比缺失多。(2)根据经验，缺失、插入和插入缺失的大小分布可以通过幂律很好地描述，即，f（k）= Ck（-B），其中f（k）是具有空位长度k的缺失、插入或插入缺失的频率，B是幂参数，并且C是归一化因子。(3)来自同一数据集的缺失和插入的B估计值彼此大致相等，表明缺失和插入的大小分布大致相同。(4)不同数据集之间的B的估计值的变化很小，表明局部结构的影响存在，但在缺失和插入的大小分布中仅起次要作用。(5)我们的分析不支持序列比对中最常用的线性空位罚分;相反，插入缺失大小分布的幂律表明适当的空位罚分是w（k）= a + B In k，其中a是差距产生成本，b1 nk是差距延伸成本。(6)缺失频率高于插入频率表明插入的差距产生成本（a（i））应大于缺失的间隙产生成本（a（d））;即a（i）- a（d）= In R，其中R是缺失与插入的频率比。
The size distributions of deletions, insertions, and indels (i.e., insertions or deletions) were studied, using 78 human processed pseudogenes and other published data sets. The following results were obtained: (1) Deletions occur more frequently than do insertions in sequence evolution; none of the pseudogenes studied shows significantly more insertions than deletions. (2) Empirically, the size distributions of deletions, insertions, and indels can be described well by a power law, i.e., f(k) = Ck(-b), where f(k) is the frequency of deletion, insertion, or indel with gap length k, b is the power parameter, and C is the normalization factor. (3) The estimates of b for deletions and insertions from the same data set are approximately equal to each other, indicating that the size distributions for deletions and insertions are approximately identical. (4) The variation in the estimates of b among various data sets is small, indicating that the effect of local structure exists but only plays a secondary role in the size distribution of deletions and insertions. (5) The linear gap penalty, which is most commonly used in sequence alignment, is not supported by our analysis; rather, the power law for the size distribution of indels suggests that an appropriate gap penalty is w(k) = a + b In k, where a is the gap creation cost and b1nk is the gap extension cost. (6) The higher frequency of deletion over insertion suggests that the gap creation cost of insertion (a(i)) should be larger than that of deletion (a(d)); that is, a(i) - a(d) = In R, where R is the frequency ratio of deletions to insertions.