CRISPRDB is an online database for genome-wide CRISPR/Cas9 gRNA design. All the gRNAs in CRISPRDB were pre-designed and predicted by a gRNA efficiency prediction model, ensemble_ridge, which was developed by assembling five high-performing gRNA design algorithms using stacking ensemble method. CRISPRDB hosts pre-designed gRNAs in two species: human, and mouse. There are three options for users to input the target gene: GenBank Accession, NCBI Gene ID or Gene Symbol. Example inputs of these three options are provided. Users could do gRNA search using our pre-designed gRNA database based on their input genes. Besides gRNA search function, users may also provide their own genomic target sequences for gRNA design using the updated prediction algorithm.
miRDB is an online database for miRNA target prediction and functional annotations. All the targets in miRDB were predicted by the bioinformatics tool MirTarget, which was developed through the analysis of thousands of miRNA-target interactions from high-throughput sequencing experiments. Common features associated with miRNA target binding have been identified and used to predict miRNA targets with machine learning methods. miRDB hosts predicted miRNA targets in five species: human, mouse, rat, dog, and chicken. As a recent update, users may provide their own sequences for customized target prediction. In addition, through combined computational analyses and literature mining, functionally active miRNAs in humans and mice have been identified. These miRNAs, as well as associated functional annotations, are presented in the FuncMir Collection in miRDB.
The CRISPR/Cas9 system lacks robust bioinformatics tools for the design of single guide RNA (sgRNA), which determines the efficacy and specificity of genome editing. We have analyzed CRISPR RNA-seq data and identified many novel features that are characteristic of highly potent sgRNAs. These features were used to develop a bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. These sgRNAs as well as the design tool are freely accessible via a web server, WU-CRISPR.
OncomiR is an online resource for exploring miRNA dysregulation in cancer. Using OncomiR, miRNAs can be queried for association with:
- Tumor stage and grade
- Cancer patient survival
- Gene targets
On-the-fly analysis can be conducted to examine:
- miRNA-based survival signatures
- Cancer type clustering by miRNA expression profile
PrimerBank is a public resource for PCR primers, containing over 306,800 primers covering most human and mouse genes. These primers are designed for gene expression detection or quantification. The primer design algorithm has been extensively tested by real-time PCR experiments for specificity and efficiency, with a design success rate of 82.6%, based on agarose gel electrophoresis.