The bulk and the tail of minimal absent words in genome sequences

doi:http://dx.doi.org/10.1088/1478-3975/13/2/026004

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	The bulk and the tail of minimal absent words in genome sequences
	Zhou, HJ; Aurell, E; Innocenti, N; Innocenti, N (reprint author), Hebrew Univ Jerusalem, Sch Comp Sci & Engn, IL-91904 Jerusalem, Israel.
刊名	PHYSICAL BIOLOGY
	2016
卷号	13 期号:2 页码:26004
关键词	Minimal Absent Words Copy-mutation Evolution Model Random Sequence
DOI	http://dx.doi.org/10.1088/1478-3975/13/2/026004
英文摘要	Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the concept of a core of a MAW, which are sequences present in the genome and closest to a given MAW. We show that in E. faecalis, E. coli and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs. We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.
学科主题	Biochemistry & Molecular Biology ; Biophysics
语种	英语
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/21704]
专题	理论物理研究所_理论物理所1978-2010年知识产出
通讯作者	Innocenti, N (reprint author), Hebrew Univ Jerusalem, Sch Comp Sci & Engn, IL-91904 Jerusalem, Israel.
推荐引用方式 GB/T 7714	Zhou, HJ,Aurell, E,Innocenti, N,et al. The bulk and the tail of minimal absent words in genome sequences[J]. PHYSICAL BIOLOGY,2016,13(2):26004.
APA	Zhou, HJ,Aurell, E,Innocenti, N,&Innocenti, N .(2016).The bulk and the tail of minimal absent words in genome sequences.PHYSICAL BIOLOGY,13(2),26004.
MLA	Zhou, HJ,et al."The bulk and the tail of minimal absent words in genome sequences".PHYSICAL BIOLOGY 13.2(2016):26004.