Resources
This page contains an overview of webservers, software and databases in relation to publications.
Current publications
Webservers
CRISPRon
CRISPR-Cas9 gRNA efficiency prediction webserver based on data integration and deep learning
Foldalign 2.5
Foldalign 2.5: Parallel version of Foldalign for structural alignment of RNA sequences
PETfold
Phylogenetic, Evolutionary and Thermodynamic folding of a multiple alignment of RNA sequences.
Software only
DisLncRF
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles
DotCoder
Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots
RPAsuite
Differential and coherent processing: Analyzing RNAseq data for pattern differences from different samples
Databases / data resources
cyanobacteria CRISPRi
This browsers show the CRISPRi-dCas9 results for a genome-wide knockdown experimental series in Synechocystis sp. PCC 6803 under 4% and 30% CO2 concentrations
Bacillus subtilis PrsA RNAseq data
RNA-seq dataset for a study of the impact of PrsA over-expression on the Bacillus subtilis transcriptome
BSGatlas
A unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access
TISSUES 2.0
Tissue expression database integrating multiple sources of evidence for human, mouse, rat and pig
Conserved RNA Structures (CRSs) in the vertebrate genome
Conserved RNA structures in vertebrate genomes
Structured RNAs in the pig genome
Annotation of structured RNAs in the pig genome by sequence, structrure homology, RNAseq data and de novo predictions
Alternative splicing in the pig
Supplementary data for the paper
Before 2010
FOLDALIGN
Pairwise local and global structural alignment of RNA sequences.
- FOLDALIGN: Pairwise local and global structural alignment of RNA sequences.
- FOLDALIGNM: Multiple global structural alignment of RNA sequences
RNA Structure Logos
Visualize the information content of DNA and RNA sequence and structure alignment
RNA genes
Supplementary material for the paper
cmf_encode
CMfinder predicted conserved RNA structures in the ENCODE regions using RNA structure constraints
PigEST
Porcine EST assembly, expression and SNP data.
- PigESTncRNA: Noncoding RNAs.
- PigESTmap: Genomic mappings.
- PigESTmito: Porcine mitochondria. Expression and SNPs.
HM ncRNA scan
Predicted conserved RNA structures in corresponding region between human and mouse unalignable in primary sequence
SRPDB
Signal recognition particle database local mirror. Includes structural alignment of the SRP RNA sequences