HIVsirDB: A Database of HIV Inhibiting siRNAs

Welcome to the official documentation for HIVsirDB, a manually curated database of short interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) responsible for silencing HIV genes. RNA interference (RNAi) is a potent candidate for the future treatment of HIV, and this database provides a comprehensive platform for researchers exploring sequence-specific inhibition of the virus. Web Server: http://crdd.osdd.net/raghava/hivsirdb/ Citation Tyagi, A., Ahmed, F., Thakur, N., Sharma, A., Raghava, G. P. S., & Kumar, M. (2011). HIVsirDB: A Database of HIV Inhibiting siRNAs. PLOS ONE, 6(11), e25945. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025917 GitHub:-https://github.com/Manish-IIITD-repository/HIVsirDB About the Platform Human immunodeficiency virus (HIV) is responsible for millions of deaths every year. Current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. HIVsirDB was created to compile and organize siRNA and shRNA data from various literature and public resources to facilitate the development of RNAi-based therapies. Database Content Extensive Repository: Contains approximately 750 siRNA/shRNA entries. Specialized Data: Includes 75 partially complementary siRNAs and over 100 escape mutant sequences. Detailed Metadata: Provides information across sixteen fields, including siRNA sequence, HIV strain, targeted genome region, efficacy, and conservation of target sequences. Key Features Search and Mapping Tools siRNAmap: A tool for mapping siRNAs onto a target sequence to visualize potential binding sites. HIVsirblast: An integrated BLAST-based tool for searching sequences against the database to find matching or similar siRNAs. Efficacy Tracking: Comprehensive information on the silencing effectiveness of each siRNA or shRNA. Biological Insights Conserved Regions: Identification of highly conserved RNA sequences of HIV-1 that serve as ideal targets for siRNA. Viral Escape Tracking: Information on escape mutants helps in designing a second generation of siRNAs that can counteract viral resistance. Technical Overview HIVsirDB is structured to provide easy access to critical inhibitory data for clinicians and bioinformaticians alike. Data Selection: Sequences were manually curated from published studies to ensure experimental validity. Lentiviral Integration: Includes information on lentiviral vectors designed for multiple shRNA expression and durable HIV-1 inhibition. Long-term Efficacy: Features data on the long-term inhibition of HIV-1 replication using RNA interference against both viral genes and cellular co-factors. Applications Therapeutic Design: Assisting in the design of potent candidates for the future treatment of HIV. Resistance Studies: Understanding viral escape mechanisms and identifying target sites less prone to mutation. Bioinformatics Research: Providing high-quality datasets for sequence-activity relationship studies and predictive modeling. Contact & Authors Manoj Kumar Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India. Email: [e-mail] License This resource is open-access and distributed under the terms of the Creative Commons Attribution License, permitting unrestricted use and distribution provided the original work is properly credited.欢迎使用HIVsirDB官方文档，这是一个经人工审核整理的小干扰RNA（short interfering RNAs, siRNAs）与短发夹RNA（short hairpin RNAs, shRNAs）数据库，其收录的序列均可靶向沉默人类免疫缺陷病毒（Human Immunodeficiency Virus, HIV）基因。RNA干扰（RNA interference, RNAi）是未来HIV治疗的极具潜力的候选策略，本数据库为探索该病毒序列特异性抑制手段的研究人员提供了全面的研究平台。 Web 服务器：http://crdd.osdd.net/raghava/hivsirdb/ 引用文献 Tyagi A, Ahmed F, Thakur N, Sharma A, Raghava GPS, Kumar M. (2011). HIVsirDB：靶向HIV的小干扰RNA数据库[J]. PLOS ONE, 6(11): e25945. 原文链接：https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025917 GitHub 仓库：https://github.com/Manish-IIITD-repository/HIVsirDB 关于本平台 人类免疫缺陷病毒（HIV）每年造成数百万例死亡。当前临床治疗需联合使用多种抗逆转录病毒药物，但此类药物因具有毒性可能对患者造成额外伤害。HIVsirDB的构建初衷是从各类已发表文献与公共数据源中整理并组织siRNA、shRNA相关数据，以推动基于RNA干扰的HIV治疗手段开发。 数据库内容 - 海量资源库：收录约750条siRNA/shRNA条目。 - 专项数据集：包含75条部分互补型siRNA以及超过100条病毒逃逸突变序列。 - 详细元数据：提供涵盖16个字段的信息，包括siRNA序列、HIV毒株、靶向基因组区域、沉默效率以及靶序列保守性等。 核心功能 搜索与比对工具 siRNAmap：一款可将siRNA映射至靶序列，以可视化潜在结合位点的工具。 HIVsirblast：一款集成BLAST功能的序列检索工具，可在数据库中查找匹配或高度相似的siRNA。 效率追踪模块：提供每条siRNA或shRNA的沉默效果的全面量化与定性信息。 生物学洞察 保守区域鉴定：筛选出HIV-1的高度保守RNA序列，此类序列可作为siRNA的理想靶向位点。 病毒逃逸追踪：收录病毒逃逸突变相关信息，可辅助设计第二代抗耐药性siRNA。 技术概览 HIVsirDB的架构设计旨在为临床医生与生物信息学家提供便捷的关键抑制数据访问途径。 数据甄选原则：所有序列均从已发表的研究中人工整理筛选，以确保实验结果的有效性与可靠性。 慢病毒载体信息：收录用于多shRNA表达、实现长效HIV-1抑制的慢病毒载体相关数据。 长期抑制效率：提供通过RNA干扰靶向病毒基因与宿主细胞辅助因子，以长期抑制HIV-1复制的相关研究数据。 应用场景 治疗方案设计：辅助开发高效的HIV治疗候选药物。 耐药性研究：解析病毒逃逸机制，鉴定不易发生突变的理想靶向位点。 生物信息学研究：为序列-活性关系研究与预测建模提供高质量的标准化数据集。 联系方式与作者 Manoj Kumar 印度昌迪加尔，CSIR微生物技术研究所生物信息学中心。邮箱：[e-mail] 版权声明 本资源为开放获取资源，遵循知识共享署名许可（Creative Commons Attribution License）协议发布，允许在明确标注原作者的前提下进行无限制的使用与分发。