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. 2012 Jan;40(Database issue):D230-6.
doi: 10.1093/nar/gkr1147. Epub 2011 Dec 1.

VIRsiRNAdb: A Curated Database of Experimentally Validated Viral siRNA/shRNA

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Free PMC article

VIRsiRNAdb: A Curated Database of Experimentally Validated Viral siRNA/shRNA

Nishant Thakur et al. Nucleic Acids Res. .
Free PMC article

Abstract

RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb.

Figures

Figure 1.
Figure 1.
VIRsiRNAdb database architecture.
Figure 2.
Figure 2.
Database statistics (a) Cell line used (b) siRNA efficacy (c) siRNA sequence matching with reference viral genomes (d) Positions of the escape mutations.
Figure 3.
Figure 3.
siTarAlign output screenshot showing the alignment of siRNA sequence with (a) family (b) virus reference genome sequences.

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