GenomeRNAi database

The GenomeRNAi database (http://www.genomernai.org) is a repository for RNAi phenotype and reagent data, aiming to provide a platform for data mining and comparisons. Data is extracted from the literature by manual curation, or directly submitted by data producers. Currently, the database contains 217 experiments in human, and 201 experiments in Drosophila, totaling to more than 1,2 million individual gene-phenotype associations. It also holds information on more than 400,000 RNAi reagents, along with quality assessment data like efficiency and specificity. The website provides functionalities for searching, browsing and downloading, and features a “frequent hitter” function as well as a functionality for the overlay of genes sharing the same phenotype onto known gene networks provided by the String database.

Predict or evaluate RNAi probes

E-RNAi is a web application that automates all tasks required for the de-novo design of RNAi probes used in small-scale and high-throughput experiments. The software predicts specific and efficient target sites for RNAi probes and suggests primer sequences for the amplification of appropriate templates.

Predict guide RNAs for Genome Editing

E-CRISP is a software tool to design and evaluate target sites for use with the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) system. The web application uses fast algorithms to identify sgRNA target sequences for use in CRISPR/Cas mediated genome editing. E-CRISP analyzes target specificity of the putative designs and assesses their genomic context (e.g. exons, transcripts, CpG islands). The design process incorporates different options of how CRISPR constructs can be used in experimental applications, such as knock-out and tagging experiments. E-CRISP can design guide RNAs for genomes of more than 30 organisms.

to top