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Analysis of correlation structures in the synechocystis PCC6803 genome
Wu ZB(武作兵)
Source PublicationComputational Biology and Chemistry
2014-12
Volume53Pages:49-58
ISSN1476-9271 
Abstract

Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is investigated to exhibit periodic and non-periodic correlation structures by using the recurrence plot method and the phase space reconstruction technique. The periodic correlation structures are generated by periodic transfer of several substrings in long periodic or non-periodic nucleotide strings embedded in the coding regions of genes. The non-periodic correlation structures are generated by non-periodic transfer of several substrings covering or overlapping with the coding regions of genes. In the periodic and non-periodic transfer, some gaps divide the long nucleotide strings into the substrings and prevent their global transfer. Most of the gaps are either the replacement of one base or the insertion/reduction of one base. In the reconstructed phase space, the points generated from two or three steps for the continuous iterative transfer via the second maximal distance can be fitted by two lines. It partly reveals an intrinsic dynamics in the transfer of nucleotide strings. Due to the comparison of the relative positions and lengths, the substrings concerned with the non-periodic correlation structures are almost identical to the mobile elements annotated in the genome. The mobile elements are thus endowed with the basic results on the correlation structures. (C) 2014 Elsevier Ltd. All rights reserved.

KeywordSynechocystis Pcc6803 Genome Correlation Structures Recurrence Plot Reconstructed Phase Space
Subject Area交叉与边缘领域的力学
Indexed BySCI ; EI
Language英语
WOS IDWOS:000347580400007
Funding OrganizationWe would like to thank the National Science Foundation for partial support through the Grant No. 11172310 and the IMECH/SCCAS SHENTENG 1800/7000 research computing facilities for assisting in the computation.
DepartmentLNM微纳米流体力学
Classification二类
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Document Type期刊论文
Identifierhttp://dspace.imech.ac.cn/handle/311007/49206
Collection非线性力学国家重点实验室
Corresponding AuthorWu ZB(武作兵)
Recommended Citation
GB/T 7714
Wu ZB. Analysis of correlation structures in the synechocystis PCC6803 genome[J]. Computational Biology and Chemistry,2014,53:49-58.
APA Wu ZB.(2014).Analysis of correlation structures in the synechocystis PCC6803 genome.Computational Biology and Chemistry,53,49-58.
MLA Wu ZB."Analysis of correlation structures in the synechocystis PCC6803 genome".Computational Biology and Chemistry 53(2014):49-58.
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