HIVsirDB: a database of HIV inhibiting siRNAs.
BACKGROUND
Human immunodeficiency virus (HIV) is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi) is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA) for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes.


METHODS
HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i) siRNAmap for mapping siRNAs on target sequence, ii) HIVsirblast for BLAST search against database, iii) siRNAalign for aligning siRNAs.


CONCLUSIONS
HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.
Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India.
Atul
A
Tyagi
Firoz
F
Ahmed
Nishant
N
Thakur
Arun
A
Sharma
Gajendra P S
GP
Raghava
Manoj
M
Kumar
D001483:Base Sequence; D019295:Computational Biology; D030541:Databases, Genetic / Q000706:statistics & numerical data; D006678:HIV / Q000378:metabolism*; D020407:Internet; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000378:metabolism*; D057386:Search Engine
D034741:RNA, Small Interfering