RNA–protein interactions: an overview
RNA binding proteins (RBPs) are key players in the regulation of gene expression. In this
chapter we discuss the main protein–RNA recognition modes used by RBPs in order to …
chapter we discuss the main protein–RNA recognition modes used by RBPs in order to …
[HTML][HTML] Predicting RNA secondary structures from sequence and probing data
RNA secondary structures have proven essential for understanding the regulatory functions
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …
The vienna RNA websuite
Abstract The Vienna RNA Websuite is a comprehensive collection of tools for folding, design
and analysis of RNA sequences. It provides a web interface to the most commonly used …
and analysis of RNA sequences. It provides a web interface to the most commonly used …
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs
Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic
regions containing potential structural ncRNAs. The analysis of these data requires highly …
regions containing potential structural ncRNAs. The analysis of these data requires highly …
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
A Busch, AS Richter, R Backofen - Bioinformatics, 2008 - academic.oup.com
Motivation: During the last few years, several new small regulatory RNAs (sRNAs) have
been discovered in bacteria. Most of them act as post-transcriptional regulators by base …
been discovered in bacteria. Most of them act as post-transcriptional regulators by base …
Improved RNA secondary structure prediction by maximizing expected pair accuracy
ZJ Lu, JW Gloor, DH Mathews - Rna, 2009 - rnajournal.cshlp.org
Free energy minimization has been the most popular method for RNA secondary structure
prediction for decades. It is based on a set of empirical free energy change parameters …
prediction for decades. It is based on a set of empirical free energy change parameters …
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs
This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting
secondary structures for multiple RNA homologs. TurboFold II augments the structure …
secondary structures for multiple RNA homologs. TurboFold II augments the structure …
The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase
Gene expression in plastids of higher plants is dependent on two different transcription
machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear …
machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear …
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure
While many RNA-binding proteins (RBPs) bind RNA in a sequence-specific manner, their
sequence preferences alone do not distinguish known target RNAs from other potential …
sequence preferences alone do not distinguish known target RNAs from other potential …
AREsite: a database for the comprehensive investigation of AU-rich elements
AR Gruber, J Fallmann, F Kratochvill… - Nucleic acids …, 2010 - academic.oup.com
AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in
vertebrate mRNA 3′-untranslated regions (UTRs). AREs are one of the most prominent cis …
vertebrate mRNA 3′-untranslated regions (UTRs). AREs are one of the most prominent cis …