Identification of a set of frequent decanucleotides in plants and in animals
Identification of a set of frequent decanucleotides in plants and in animals
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植物和动物中一组常见十核苷酸的鉴定
DOI：
10.1093/bioinformatics/10.5.465
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发表时间：
1994
期刊：
影响因子：
--
通讯作者：
I. Barrai
中科院分区：
文献类型：
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作者：
C. Scapoli;A. Rodriguez;S. Volinia;M. Beretta;I. Barrai
为了检测转录控制信号，我们研究了从GenBank 71.0中提取的635个序列组成的1.961 Mbase植物基因样本中1，048，576个10 bp长的寡核苷酸的频率分布。在所有十聚体中，3255或0.3%的频率比平均值高10倍，并进行进一步的统计分析。对于3255个十聚体（亲本）中的每一个，我们计算了与亲本相差一个碱基突变的30个十聚体（后代）的个体频率，并计算了后代的两个方差/平均卡方，有和没有亲本十聚体。通过研究两个卡方之间的比率的分布，我们观察到在3255个频率高于平均值10倍的十聚体中，432个具有卡方比率> 1.9。在这个剩余的集合中，对应于所有可能的十聚体的<0.04%，只发现了15个已知的真核转录控制元件;另一方面，它包括29个与一组果蝇的十核苷酸匹配的十核苷酸，24个与一组哺乳动物的十核苷酸匹配，其中13个用一组酵母菌，4个用一组病毒--所有的组都是用这里描述的统计程序鉴定的。这些decanucloetides是高度重复的，似乎存在于所有高等生物，而它们是罕见的哺乳动物病毒。
We studied the frequency distribution of 1,048,576 oligonucleotides 10 bp long in a sample of 1.961 Mbase of genes from plants, made of 635 sequences extracted from GenBank 71.0, with the aim of detecting transcription control signals. Among all decamers, 3255, or 0.3%, had a frequency 10 times higher than the mean and were subjected to further statistical analysis. For each of the 3255 decamers (parents), we counted the individual frequencies of the 30 decamers (progeny) differing from the parent by one base mutation, and calculated two variance/mean chi-squares for the progeny, with and without the parent decamer. By studying the distribution of the ratio between the two chi-squares we observed that out of 3255 decamers > 10 times frequent than average, 432 had a chi-square ratio > 1.9. In this residual set, which corresponds to < 0.04 per cent of all possible decamers, only 15 known eukaryotic transcription control elements were found; on the other hand, it included 29 decanucleotides that matched with decanucleotides of a set of Drosophila, 24 with a set from mammals, 13 with a set from yeast and four with a set of viruses--all sets identified with the statistical procedures here described. These decanucloetides are highly repetitive and seem to be present throughout all higher organisms, whereas they are uncommon in mammalian viruses.