- quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates on short read RNA-seq datasets
- automated annotation of Metazoan mitochondrial genomes
- produce overview maps of evolutionary conserved splice sites
- analysis of small nucleolar RNAs (snoRNAs) in fungi genomes Databases
- Transfer RNA Database contains more than 12.000 tRNA genes and about 600 tRNA sequences of 587 species
Tools for download:
Vienna RNA Package
- Folding and comparing RNA secondary structures.
- Detect blocks of overlapping reads using a gaussian-distribution approach
- Gene finding via semi-global alignment
- An algorithm for prediction of RNA folding trajectories.
- Detection of tertiary motifs in RNA secondary structure and sequence
- Target prediction for Box C/D snoRNAs
- Predicts reading direction of structured RNAs in multiple sequence alignments.
- RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs.
- RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence.
- fast short read mapping with indels.