RBC Services

RNA structure prediction and analysis, prediction of ncRNA targets, definition and classification of RNA transcripts, analysis of RNA-protein interactions, genome-wide annotation of secondary structures via classification of regulatory RNAs.
RBC will offer Galaxy support for all interested units. This involves among other things also the organisation of Galaxy user and developer workshops.

Freiburg RNA Tools Webserver

RNA local sequence-structure alignment (LocARNA), inverse folding (INFO-RNA), RNA-RNA interaction (IntaRNA), sRNA target prediction (CopraRNA), fixed sequence structure alignment (MARNA), clustering and prediction of repeat conservation (CRISPR), RNA sequence design (antaRNA),motif based comparison and alignment (ExpaRNA), structure ensemble multiple alignment (CARNA). Find this service in BioTools here.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

Freiburg Galaxy Server

> 200 registered users, > 900 bioinformatics tools - a large portion of which are tools for RNA analysis. 2K cores, 1TB RAM. > 30 published workflows, histories and data libraries. The server also hosts a collection of pages/tutorials for training and education detailing NGS methods and RNA analysis as well as useful literature and galaxy use guides.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

Freiburg tools (download)

RNA motif search (memeris), bioinformatic utility and energy landscape libraries, RNA energy landscape tools, sequence alignment, local folding, structural clustering of RNAs, RNA-protein binding preference modeling and prediction, exact pattern matching in RNA sequence ensemble, constraint based atom-atom mapping, machine learning for bioinformatics (EDeN).

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

Docker images: galaxy-stable, galaxy-rna-workbench

> 2200 downloads, Github repository based autobuilt extensible Docker image, built on Ubuntu - providing a scalable Galaxy instance that includes: PostgreSQL, Nginx, uwsgi, proFTP, supervisord, SLURM, Ansible roles and Docker in Docker. Provides access to many NGS and RNA tools, visualisations, interactive environemnts (e.g. IPython) as well as various utilities, reference genomes and data libraries.

Website
Contact

Github repository: galaxytools

Provides galaxy datatypes and tool packages, visualisations, workflows and > 300 galaxy tool wrappers. This repository is under constant development by ~25 contributors and serves as a central point for integrating new RNA tools into the Freiburg Galaxy Server and galaxy-rna-workbench.

Website
Contact

Bioinformatics Leipzig

Webservices:

DARIO
- quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates on short read RNA-seq datasets

MITOS
- automated annotation of Metazoan mitochondrial genomes

SpliceMap
- produce overview maps of evolutionary conserved splice sites

snoStrip
- analysis of small nucleolar RNAs (snoRNAs) in fungi genomes Databases

tRNAdb
- 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.

blockbuster
- Detect blocks of overlapping reads using a gaussian-distribution approach

GotohScan
- Gene finding via semi-global alignment

Kinwalker
- An algorithm for prediction of RNA folding trajectories.

motifSearch
- Detection of tertiary motifs in RNA secondary structure and sequence

PLEXY
- Target prediction for Box C/D snoRNAs

RNAstrand
- Predicts reading direction of structured RNAs in multiple sequence alignments.

RNAplex
- RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs.

RNAsnoop
- RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence.

segemehl
- fast short read mapping with indels.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

MDC-Berlin: Ohler Lab

Recent and ongoing projects address transcription control (initiation, modeling of enhancers and their evolution, regulatory site identification, decoding enhancers based on sequence and chromatin), small RNAs (identification of microRNAs and targets), expression (condition-specific microarray/sequencing data, spatial expression from microscopy), or the modeling of regulatory networks containing transcription factors and miRNAs.

Tools for download:
Prediction of coding and non-coding genes RSVP
- prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads

PIPmiR
- identify novel plant miRNA genes from a combination of deep sequencing data and genomic features

NASTIseq
- identification of cis-Natural Antisense Transcripts (cis-NAT) using strand specific RNA-seq data Promoter and enhancer analysis

S-Peaker
- identify probable locations for single-peak TSSs in an input sequence Orthologous enhancers
- searches for orthologous enhancer region in a related species for a given known enhancer miRNA target prediction

MUMMIE
- MUltivariate Markov Modeling Inference Engine

microMUMMIE
- microRNA target-site prediction in PAR-CLIP data

TargetThermo
- compute predicted expression fold change of a gene caused by a miRNA

WaRSwap
- network motif discovery in large multi-layer networks that include Transcription Factors (TFs), microRNAs (miRNAs), and non-TF protein coding genes. 

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

MDC-Berlin: Rajewsky Lab

Focus on post-transcriptional gene regulation by small RNAs (for example microRNAs) and RNA binding proteins.

Web-services:

PicTar
- identification of microRNA targets Databases

doRiNA
- RNA interactions in post-transcriptional regulation. Find this service in BioTools here.

circBase (contact: This email address is being protected from spambots. You need JavaScript enabled to view it.)
- explore public circRNA datasets and download tools to discover circRNAs in RNA-seq data

pSILAC
- Genome-wide changes in protein synthesis induced by microRNAs

Tools for download:

miReduce
- motif based fold change profile of genome wide expression levels

Discrover
- motif discovery method to find binding sites of nucleic acid binding proteins

RNA competition
- competition between target sites of regulators shapes post-transcriptional gene regulation.

Website

de.STAIR-Leipzig

Tools for download:

  • segemehl - short read mapping with gaps

  • metilene - Fast and sensitive detection of differential DNA methylation

  • haarz - A simple data-adaptive probabilistic variant caller

Website
Contact

epi-Berlin

Tools for download:

  • genomation - a package for summary and annotation of genomic intervals

  • methylKit - a package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing

Website
Contact

de.STAIR-Rostock

TRAPLINE (Transparent, Reproducible and Automated analysis PipeLINE) is an RNAseq data processing, evaluation, and prediction tool optimized for Illumina FASTQ reads, and other sequencing platforms like SOLiD or Solexa. Predictions are based on modules which are able to identify protein-protein interactions, miRNA targets and alternatively splicing variants or promoter enriched sites. TRAPLINE is available in the Galaxy web platform

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.

de.STAIR-Rostock

The TriplexRNA is a database of cooperating miRNAs and their mutual targets which enables researchers to explore novel patterns in gene regulation.

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.