Berlin RNA Toolbox
The Berlin RNA Toolbox is a comprehensive collection of bioinformatics tools and databases. The toolbox offers a wide range of resources for researchers to analyze, predict, and understand various aspects of RNA biology.
Key Benefits
- Comprehensive analysis of RNA interactions : Identify potential binding sites of microRNAs on messenger RNAs (mRNAs) and explore the complex relationships between RNAs.
- In-depth analysis of circular RNAs : Discover circRNAs in RNA-seq data and explore their potential functions.
- Accurate prediction of protein-RNA interactions : Identify specific binding regions between proteins and RNAs.
Tools
- PicTar : A microRNA target predictor that identifies potential binding sites of microRNAs on messenger RNAs (mRNAs).
- 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, helping to identify specific binding regions between proteins and RNAs.
- microMUMMIE : MicroRNA target-site prediction in PAR-CLIP data, allowing researchers to predict potential microRNA binding sites within PAR-CLIP peaks.
- cERMIT : A motif finder for large sequence sets e.g. from chromatin or RNA immunoprecipitation experiments, enabling users to identify conserved motifs across different sequences.
Databases
- doRiNA : A database of RNA interactions in post-transcriptional regulation, providing insights into the complex relationships between RNAs.
- circBase : A database for public circular RNA datasets, allowing users to discover circRNAs in RNA-seq data and explore their potential functions.
Target Audience
The Berlin RNA Toolbox is designed for researchers in the fields of molecular biology, bioinformatics, and computational biology. The tools and databases provided are particularly useful for scientists interested in understanding various aspects of RNA biology, including microRNA regulation, circular RNAs, and protein-RNA interactions.