Berlin RNA toolbox

deNBI RNA Bioinformatics Centre Berlin node provides several tools for RNA bioinformatics. The tools provided are listed below.

Databases

doRiNA: a database of RNA interactions in post-transcriptional regulation

circBase: a database for public circular RNA datasets and tools to discover circRNAs in RNA-seq data; PicTar: a microRNA target predictor; miRDeep: a probabilistic model that detects the presence of expressed animal microRNAs in deep sequencing data;

Tools

PicTar: a microRNA target predictor;

miRDeep: a probabilistic model that detects the presence of expressed animal microRNAs in deep sequencing data;

PIPmiR: a tool to identify novel plant miRNA genes from a combination of deep sequencing and genomic features;

NASTIseq: expression analysis for the identification of cis-Natural Antisense Transcripts (cis-NAT) from strand specific RNA-seq data;

PARalyzer: a peak finder for protein- RNA interaction sites in PAR-CLIP data; microMUMMIE: microRNA target-site prediction in PAR-CLIP data

cERMIT: a motif finder for large sequence sets e.g. from chromatin or RNA immunopreciptation experiments.