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.