完整RNA病毒基因组中保守RNA结构元件的自动检测
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
作者信息
Hofacker I L, Fekete M, Flamm C, Huynen M A, Rauscher S, Stolorz P E, Stadler P F
机构信息
Institut für Theoretische Chemie, Universität Wien, Wien, Austria, EMBL, Heidelberg, Germany, Max Delbrück Center, Berlin, Germany.
出版信息
Nucleic Acids Res. 1998 Aug 15;26(16):3825-36. doi: 10.1093/nar/26.16.3825.
Abstract
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of approximately 10 sequences, efficiently exploiting the information contained in the sequence variability. The procedure constructs a prediction only for those parts of sequences that are consistent with a single conserved structure. Our implementation produces reasonable consensus structures without user interference. As an example we have analysed the complete HIV-1 and hepatitis C virus (HCV) genomes as well as the small segment of hantavirus. Our method confirms the known structures in HIV-1 and predicts previously unknown conserved RNA secondary structures in HCV.
摘要
我们提出了一种在一族相关RNA序列中检测保守RNA二级结构的新方法。我们的方法基于热力学结构预测和系统发育比较的结合。与纯系统发育方法不同，我们的算法可用于大约10个序列的小数据集，有效利用序列变异性中包含的信息。该程序仅对与单个保守结构一致的序列部分构建预测。我们的实现无需用户干预即可生成合理的共有结构。作为一个例子，我们分析了完整的HIV-1和丙型肝炎病毒（HCV）基因组以及汉坦病毒的小片段。我们的方法证实了HIV-1中已知的结构，并预测了HCV中以前未知的保守RNA二级结构。
相似文献
1
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.完整RNA病毒基因组中保守RNA结构元件的自动检测
Nucleic Acids Res. 1998 Aug 15;26(16):3825-36. doi: 10.1093/nar/26.16.3825.
2
Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA.丙型肝炎病毒基因组RNA 3'末端保守98个碱基序列的二级结构测定
J Virol. 1997 Oct;71(10):7345-52. doi: 10.1128/JVI.71.10.7345-7352.1997.
3
Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.丙型肝炎病毒全基因组比对中保守 RNA 二级结构的综合调查。
Sci Rep. 2024 Jul 2;14(1):15145. doi: 10.1038/s41598-024-62897-0.
4
Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus.丙型肝炎病毒编码区RNA二级结构的热力学与系统发育预测
RNA. 2002 Jun;8(6):824-41. doi: 10.1017/s1355838202554066.
5
Automatic detection of conserved base pairing patterns in RNA virus genomes.RNA病毒基因组中保守碱基配对模式的自动检测
Comput Chem. 1999 Jun 15;23(3-4):401-14. doi: 10.1016/s0097-8485(99)00013-3.
6
Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein.保守二级结构的热力学预测：应用于HIV的RRE元件、CMV的tRNA样元件和朊病毒蛋白的mRNA。
J Mol Biol. 1996 May 24;258(5):813-26. doi: 10.1006/jmbi.1996.0289.
7
Phylogenetic evidence for the improved RNA higher-order structure in internal ribosome entry sequences of HCV and pestiviruses.丙型肝炎病毒和瘟病毒内部核糖体进入序列中RNA高阶结构改善的系统发育证据。
Virus Genes. 1998;17(3):279-95. doi: 10.1023/a:1008073905920.
8
Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.三种与HIV相关的RNA基因组的基于结构的比对和共有二级结构
PLoS Comput Biol. 2015 May 20;11(5):e1004230. doi: 10.1371/journal.pcbi.1004230. eCollection 2015 May.
9
A phylogenetically conserved stem-loop structure at the 5' border of the internal ribosome entry site of hepatitis C virus is required for cap-independent viral translation.丙型肝炎病毒内部核糖体进入位点5'边界处的一个系统发育保守的茎环结构是病毒不依赖帽状结构进行翻译所必需的。
J Virol. 1999 Feb;73(2):1165-74. doi: 10.1128/JVI.73.2.1165-1174.1999.
10
Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs.丙型肝炎病毒和瘟病毒基因组RNA 5'非翻译区的二级结构
Nucleic Acids Res. 1992 Oct 11;20(19):5041-5. doi: 10.1093/nar/20.19.5041.
引用本文的文献
1
Review of machine learning methods for RNA secondary structure prediction.机器学习方法在 RNA 二级结构预测中的研究进展综述。
PLoS Comput Biol. 2021 Aug 26;17(8):e1009291. doi: 10.1371/journal.pcbi.1009291. eCollection 2021 Aug.
2
Musashi binding elements in Zika and related Flavivirus 3'UTRs: A comparative study in silico.寨卡及相关黄病毒 3'UTR 中的 Musashi 结合元件：计算机比较研究。
Sci Rep. 2019 May 6;9(1):6911. doi: 10.1038/s41598-019-43390-5.
3
An algebraic language for RNA pseudoknots comparison.用于 RNA 假结比较的代数语言。
BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):161. doi: 10.1186/s12859-019-2689-5.
4
Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses.蜱传、昆虫特异且无已知媒介的黄病毒 3'UTR 中的功能 RNA 结构。
Viruses. 2019 Mar 24;11(3):298. doi: 10.3390/v11030298.
5
Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.全球范围内HIV/SIV包膜糖蛋白gp120 RNA在感染宿主内及宿主间的结构与进化评估。
Virus Evol. 2018 Jun 21;4(1):vey018. doi: 10.1093/ve/vey018. eCollection 2018 Jan.
6
The 5BSL3.2 Functional RNA Domain Connects Distant Regions in the Hepatitis C Virus Genome.5BSL3.2功能性RNA结构域连接丙型肝炎病毒基因组中的远距离区域。
Front Microbiol. 2017 Oct 31;8:2093. doi: 10.3389/fmicb.2017.02093. eCollection 2017.
7
A conserved RNA structural element within the hepatitis B virus post-transcriptional regulatory element enhance nuclear export of intronless transcripts and repress the splicing mechanism.乙肝病毒转录后调控元件内的一个保守RNA结构元件可增强无内含子转录本的核输出并抑制剪接机制。
Mol Biol Rep. 2015 Dec;42(12):1603-14. doi: 10.1007/s11033-015-3928-0. Epub 2015 Oct 29.
8
In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1.甲型H1N1流感病毒神经氨酸酶抑制剂奥司他韦的计算机模拟修饰
J Biomed Res. 2015 Apr;29(2):150-9. doi: 10.7555/JBR.29.20130024. Epub 2014 Dec 12.
9
cis-Acting RNA elements in the hepatitis C virus RNA genome.丙型肝炎病毒RNA基因组中的顺式作用RNA元件。
Virus Res. 2015 Aug 3;206:90-8. doi: 10.1016/j.virusres.2014.12.029. Epub 2015 Jan 7.
10
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.真核单链DNA病毒基因组中普遍存在的具有生物学功能的二级结构的证据。
J Virol. 2014 Feb;88(4):1972-89. doi: 10.1128/JVI.03031-13. Epub 2013 Nov 27.
本文引用的文献
1
Spontaneous and engineered deletions in the 3' noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of a flavivirus.蜱传脑炎病毒3'非编码区的自发和工程缺失：黄病毒高度减毒突变体的构建
J Virol. 1998 Mar;72(3):2132-40. doi: 10.1128/JVI.72.3.2132-2140.1998.
2
Determination of the secondary structure of and cellular protein binding to the 3'-untranslated region of the hepatitis C virus RNA genome.丙型肝炎病毒RNA基因组3'非翻译区二级结构及细胞蛋白结合的测定
J Virol. 1997 Nov;71(11):8698-706. doi: 10.1128/JVI.71.11.8698-8706.1997.
3
Automated alignment of RNA sequences to pseudoknotted structures.RNA序列与假结结构的自动比对。
Proc Int Conf Intell Syst Mol Biol. 1997;5:311-8.
4
Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA.丙型肝炎病毒基因组RNA 3'末端保守98个碱基序列的二级结构测定
J Virol. 1997 Oct;71(10):7345-52. doi: 10.1128/JVI.71.10.7345-7352.1997.
5
6
Mismatch base pairs in RNA.RNA中的错配碱基对。
Prog Nucleic Acid Res Mol Biol. 1997;57:1-39. doi: 10.1016/s0079-6603(08)60276-7.
7
Assessing the reliability of RNA folding using statistical mechanics.使用统计力学评估RNA折叠的可靠性。
J Mol Biol. 1997 Apr 18;267(5):1104-12. doi: 10.1006/jmbi.1997.0889.
8
Variation of the hepatitis C virus 5' non-coding region: implications for secondary structure, virus detection and typing. The International HCV Collaborative Study Group.丙型肝炎病毒5'非编码区的变异：对二级结构、病毒检测和分型的影响。国际丙型肝炎病毒协作研究组
J Gen Virol. 1995 Jul;76 ( Pt 7):1749-61. doi: 10.1099/0022-1317-76-7-1749.
9
10
Base pairing probabilities in a complete HIV-1 RNA.完整HIV-1 RNA中的碱基配对概率。
J Comput Biol. 1996 Summer;3(2):253-74. doi: 10.1089/cmb.1996.3.253.
Zotero 插件