What is the RNAStructuromeDB?
Frequently Asked Questions
Abbreviated Question:
What is the RNAStructuromeDB?
Search results
Rfam
Resource
"The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs)."
What is JBrowse?
Frequently Asked Questions
Abbreviated Question:
What is JBrowse?
Answer:
We do! Here is a user guide specifically for RNAStructuromeDB: jbrowse.pdf
JBrowse is freely available as part of the generic model organism database project (GMOD) and guides can be found there as well: http://gmod.org/wiki/JBrowse
How to Cite
Page
If you use this work please cite:
RNAStructuromeDB
R.J. Andrews, L. Baber, W.N. Moss (2017), "RNAStructuromeDB: A genome-wide database for RNA structural inference." Scientific Reports. 7. . 10.1038/s41598-017-17510-y.
Folding algorithms Read more about How to Cite
What is the RNAStructuromeDB?
Frequently Asked Questions
Abbreviated Question:
What is the RNAStructuromeDB?
Answer:
You can read about the RNA Structurome DB here: Andrews RJ, Baber L, and Moss W. Sci Rep. 2017.
Pathogens
Page
A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs.
Page
There are 9 herpesviruses known to infect humans, of which Epstein–Barr virus (EBV) is the most widely distributed (>90% of adults infected). This ubiquitous virus is implicated in a variety of cancers and autoimmune diseases. Previous analyses of the EBV genome revealed numerous regions with evidence of generating unusually stable and conserved RNA secondary structures and led to the discovery of a novel class of EBV non-coding (nc)RNAs: the stable intronic sequence (sis)RNAs. Read more about A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs.
SARS-CoV-2 Structure Extracts
Page
The ScanFold approach defines specific motifs of likely function. All predicted motifs containing at least one base pair with an average Zavg < -1 have been modeled, annotated, and compiled into individual PDF files for easy viewing.
structures_zavg-1.pdf Read more about SARS-CoV-2 Structure Extracts
SARS-CoV-2 Global Model Comparisons
Page
The base pairing (BP) tracks for the in silico and reactivity constrained ScanFold models generated in the paper “A map of the SARS-CoV-2 functional RNA Structurome.” are viewable (via the IGV app) by following the link below. Additionally, the BP structure tracks for the Manfredonia et al. and Huston et al. reactivity-informed models are also viewable as are the reactivity datasets (in the form of a .wig track) from the Manfredonia et al., Huston et al. and Sun et al. structure probing experiments.
IGV.js Global Model Comparisons Read more about SARS-CoV-2 Global Model Comparisons