siVirus：用于高度分化病毒序列的基于网络的抗病毒小干扰RNA设计软件。

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.

作者信息

Naito Yuki, Ui-Tei Kumiko, Nishikawa Toru, Takebe Yutaka, Saigo Kaoru

机构信息

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan.

出版信息

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W448-50. doi: 10.1093/nar/gkl214.

DOI:10.1093/nar/gkl214

PMID:16845046

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1538817/

Abstract

siVirus (http://siVirus.RNAi.jp/) is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. These siRNAs are expected to resist viral mutational escape, since their highly conserved targets likely contain structurally/functionally constrained elements. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health.

摘要

siVirus（http://siVirus.RNAi.jp/）是一个基于网络的在线软件系统，可为抗病毒RNA干扰（RNAi）提供高效的小干扰RNA（siRNA）设计。siVirus搜索针对不同病毒序列高度保守区域的功能性、脱靶效应最小化的siRNA。这些siRNA有望抵抗病毒的突变逃逸，因为它们高度保守的靶标可能包含结构/功能受限的元件。siVirus将成为设计针对高度不同病原体（包括对全球人类健康构成巨大威胁的人类免疫缺陷病毒（HIV）、丙型肝炎病毒（HCV）、流感病毒和严重急性呼吸综合征冠状病毒）的最佳siRNA的有用工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/84e3/1538817/d320d4e9e255/gkl214f1.jpg

相似文献

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W448-50. doi: 10.1093/nar/gkl214.

dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W589-91. doi: 10.1093/nar/gki419.

HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome.

Nucleic Acids Res. 2005 Feb 1;33(2):796-804. doi: 10.1093/nar/gki220. Print 2005.

A novel program to design siRNAs simultaneously effective to highly variable virus genomes.

Biochem Biophys Res Commun. 2009 Jul 10;384(4):431-5. doi: 10.1016/j.bbrc.2009.04.143. Epub 2009 May 5.

A protocol for designing siRNAs with high functionality and specificity.

Nat Protoc. 2007;2(9):2068-78. doi: 10.1038/nprot.2007.278.

TROD: T7 RNAi Oligo Designer.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W121-3. doi: 10.1093/nar/gkh360.

Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape.

J Virol. 2005 Feb;79(3):1645-54. doi: 10.1128/JVI.79.3.1645-1654.2005.

siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W124-9. doi: 10.1093/nar/gkh442.

Effective inhibition of hepatitis B virus replication by small interfering RNAs expressed from human foamy virus vectors.

Int J Mol Med. 2007 Apr;19(4):705-11.

Optimal design and validation of antiviral siRNA for targeting hepatitis B virus.

Acta Pharmacol Sin. 2008 Dec;29(12):1522-8. doi: 10.1111/j.1745-7254.2008.00891.x.

引用本文的文献

Therapeutic Approaches of Viral Gene Silencing by Small Interfering RNA: Strategies to Prevent the Emergence of Antiviral Resistant Escape Mutants.

Pharmaceuticals (Basel). 2025 Jul 1;18(7):987. doi: 10.3390/ph18070987.

In Silico and In Vitro development of novel small interfering RNAs (siRNAs) to inhibit SARS-CoV-2.

Comput Struct Biotechnol J. 2025 Mar 23;27:1460-1471. doi: 10.1016/j.csbj.2025.03.034. eCollection 2025.

Small interfering RNA (siRNA)-based therapeutic applications against viruses: principles, potential, and challenges.

J Biomed Sci. 2023 Oct 16;30(1):88. doi: 10.1186/s12929-023-00981-9.

Efficient Inhibition of HIV Using CRISPR/Cas13d Nuclease System.

Viruses. 2021 Sep 16;13(9):1850. doi: 10.3390/v13091850.

In Vitro Inhibitory Analysis of Rationally Designed siRNAs against MERS-CoV Replication in Huh7 Cells.

Molecules. 2021 Apr 29;26(9):2610. doi: 10.3390/molecules26092610.

Viral Vectors Applied for RNAi-Based Antiviral Therapy.

Viruses. 2020 Aug 23;12(9):924. doi: 10.3390/v12090924.

Efficient Inhibition of Avian and Seasonal Influenza A Viruses by a Virus-Specific Dicer-Substrate Small Interfering RNA Swarm in Human Monocyte-Derived Macrophages and Dendritic Cells.

J Virol. 2019 Feb 5;93(4). doi: 10.1128/JVI.01916-18. Print 2019 Feb 15.

A review on current status of antiviral siRNA.

Rev Med Virol. 2018 Jul;28(4):e1976. doi: 10.1002/rmv.1976. Epub 2018 Apr 15.

In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes.

PLoS One. 2016 Jul 21;11(7):e0159211. doi: 10.1371/journal.pone.0159211. eCollection 2016.

Precise and efficient siRNA design: a key point in competent gene silencing.

Cancer Gene Ther. 2016 Apr;23(4):73-82. doi: 10.1038/cgt.2016.4. Epub 2016 Mar 18.

本文引用的文献

GenBank.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D16-20. doi: 10.1093/nar/gkj157.

Antiviral RNAi therapy: emerging approaches for hitting a moving target.

Gene Ther. 2006 Mar;13(6):532-40. doi: 10.1038/sj.gt.3302645.

Induction and suppression of RNA silencing: insights from viral infections.

Nat Rev Genet. 2005 Mar;6(3):206-20. doi: 10.1038/nrg1555.

Accelerated off-target search algorithm for siRNA.

Bioinformatics. 2005 Apr 15;21(8):1316-24. doi: 10.1093/bioinformatics/bti155. Epub 2004 Nov 25.

Noise amidst the silence: off-target effects of siRNAs?

Trends Genet. 2004 Nov;20(11):521-4. doi: 10.1016/j.tig.2004.08.006.

The Los Alamos hepatitis C sequence database.

Bioinformatics. 2005 Feb 1;21(3):379-84. doi: 10.1093/bioinformatics/bth485. Epub 2004 Sep 17.

Unlocking the potential of the human genome with RNA interference.

Nature. 2004 Sep 16;431(7006):371-8. doi: 10.1038/nature02870.

Revealing the world of RNA interference.

Nature. 2004 Sep 16;431(7006):338-42. doi: 10.1038/nature02872.

siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W124-9. doi: 10.1093/nar/gkh442.

An algorithm for selection of functional siRNA sequences.

Biochem Biophys Res Commun. 2004 Apr 16;316(4):1050-8. doi: 10.1016/j.bbrc.2004.02.157.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验

siVirus：用于高度分化病毒序列的基于网络的抗病毒小干扰RNA设计软件。

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.

作者信息

机构信息

出版信息

相似文献

引用本文的文献

本文引用的文献

文献AI研究员

用中文搜PubMed

文档翻译

Suppr 超能文献

siVirus：用于高度分化病毒序列的基于网络的抗病毒小干扰RNA设计软件。

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences.

作者信息

机构信息

出版信息

相似文献

引用本文的文献

本文引用的文献