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A database of siRNAs experimentally tested by researchers with consistent efficacy ratings. This database will help siRNA researchers develop more reliable siRNA design rules; in the meantime, siRecords will benefit experimental researchers directly by providing them with information about the siRNAs that have been experimentally tested against the genes of their interest. The current release of siRecords contains the records of 17,192 RNAi experiments targeting 5,086 genes. Data contributors could submit their own records of RNAi experiments.
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.
NSDNA / Nervous System Disease NcRNAome Atlas
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.
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 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.
EbolaVCR / Ebola Virus Computational Resources
In silico resources developed to facilitate scientific community fighting against deadly virus EBOLA. EbolaVCR enlists possible vaccine candidates, therapeutic siRNAs and other related resources. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses.
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.
HuSiDa / Human siRNA Database
Provides sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments, including the mode of siRNA generation, recipient cell lines, transfection reagents and procedures and direct links to published references (PubMed). To retrieve functional siRNAs sequences for a specific gene, the human siRNA database can be searched for UniGene cluster IDs, gene names, RefSeq accession numbers and target gene descriptions.
Provides a gene-centric view of siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by a combination of methods. Linked to these sequences is information such as siRNA thermodynamic properties and the potential for sequence-specific off-target effects. The database interface was designed with the experimental user group as the primary target audience. The user interface is gene-centric, allowing the user to search by nucleotide accession number, free text, sequence or by viewing the list of genes with verified siRNAs.
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