How independent are the appearances of n-mers in different genomes?
How independent are the appearances of n-mers in different genomes?
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DOI：
10.1093/bioinformatics/bth266
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发表时间：
2004-10-12
期刊：
影响因子：
5.8
通讯作者：
Pettitt, BM
中科院分区：
文献类型：
--
作者：
Fofanov, Y;Luo, Y;Pettitt, BM
研究动机：DNA序列的统计特性分析对于进化生物学以及DNA探针和PCR技术都很重要。反过来，这些技术可用于生物体鉴定，这意味着在传染病诊断、环境研究等方面的应用。我们目前的相关性分析的结果分布的存在/不存在的短核苷酸序列的不同长度（“n-mers”，n = 5 - 20），以及多细胞生物（包括人类）的五个基因组。我们计算给定的n-mer在给定的基因组中是否存在（存在频率），这不是通常计算的n-mer在一个或多个基因组中出现的次数（出现频率）。对于彼此不是近亲的生物体，其基因组中不同7- 20聚体的存在/不存在是不相关的。对于生物学上的近亲，在这个范围内出现了一些与n-mer存在的相关性，但没有预期的那么强。不同基因组中存在的n-mer之间的抑制相关性导致使用随机n-mer组（具有适当选择的n）来区分不同生物体的基因组和可能的相同物种（包括人类）的个体基因组的可能性，具有低的错误概率。
Motivation: Analysis of statistical properties of DNA sequences is important for evolutional biology as well as for DNA probe and PCR technologies. These technologies, in turn, can be used for organism identification, which implies applications in the diagnosis of infectious diseases, environmental studies, etc.Results: We present results of the correlation analysis of distributions of the presence/absence of short nucleotide subsequences of different length ('n-mers', n = 5 - 20) in more than 1500 microbial and virus genomes, together with five genomes of multicellular organisms (including human). We calculate whether a given n-mer is present or absent (frequency of presence) in a given genome, which is not the usually calculated number of appearances of n-mers in one or more genomes (frequency of appearance). For organisms that are not close relatives of each other, the presence/absence of different 7-20mers in their genomes are not correlated. For close biological relatives, some correlation of the presence of n-mers in this range appears, but is not as strong as expected. Suppressed correlations among the n-mers present in different genomes leads to the possibility of using random sets of n-mers (with appropriately chosen n) to discriminate genomes of different organisms and possibly individual genomes of the same species including human with a low probability of error.