Small interfering RNA databases | Non-coding transcript data analysis

Centralizes 24 nucleotide small interfering RNA (24-nt siRNA) loci and information, including fundamental locus information, expression profiles and annotation of transposon elements, from next-generation sequencing (NGS) data for 10 popular plant species. Pln24NT provides an intuitive web interface for convenient searching and browsing. Furthermore, analytical tools were included to help users flexibly analyze their own siRNA NGS data. Pln24NT will help the plant research community to discover and characterize 24-nt siRNAs, and may prove useful for studying the roles of siRNA in RNA-directed DNA methylation in plants.

A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents a useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.

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. It is possible to perform a quick search based on various database fields i.e. Virus name, siRNA sequence, target region, cell line and Pubmed ID.

A specialized databank for chemically modified siRNAs. siRNAmod contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. siRNAmod browsing option helps user to surf via these five categories: i) modification in sense strand, ii) position of modification in sense strand, iii) modification in antisense strand, iv) position of modification in antisense strand and v) reference.

A manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. Users can explore information in user friendly manner using the search and browsing facility. HIVsirDB is useful to experimentalists in deciding the highly potent siRNAs targeting the most susceptible target site in HIV genome and its experimental procedure to suppress HIV infection.

Offers information about 2 million products, submitted by a reagent provider partners. All reagents are organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones, biochemicals, and others). VAD is developed with manually curation antibody applications from selected formal publications. Review articles for antibodies, based on VAD, and for commonly used reagents are freely available.

Facilitates the design of vector-based small interference RNA (siRNA) and siRNA cassette. GenScript's siRNA Design Center provides second generation siRNA design tool, that consists of a siRNA target finder, a siRNA construct builder and a siRNA sequence scramble. To protect users’ privacy, the programs are hosted on a secure Web server.