Design of RNAs: comparing programs for inverse RNA folding
Computational programs for predicting RNA sequences with desired folding properties have
been extensively developed and expanded in the past several years. Given a secondary …
been extensively developed and expanded in the past several years. Given a secondary …
Alternate RNA structures
MTP Wu, V D'Souza - Cold Spring Harbor Perspectives …, 2020 - cshperspectives.cshlp.org
SUMMARY RNA molecules fold into complex three-dimensional structures that sample
alternate conformations ranging from minor differences in tertiary structure dynamics to …
alternate conformations ranging from minor differences in tertiary structure dynamics to …
Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences
S Mukherjee, S Sengupta - Bioinformatics, 2016 - academic.oup.com
Riboswitches are non-coding RNA located in the 5′ untranslated regions where they bind
a target metabolite used to specify the riboswitch class and control the expression of …
a target metabolite used to specify the riboswitch class and control the expression of …
An archaeal fluoride-responsive riboswitch provides an inducible expression system for hyperthermophiles
MC Speed, BW Burkhart, JW Picking… - Applied and …, 2018 - Am Soc Microbiol
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated the
overexpression of native genes, enabled the addition of sequences encoding secretion …
overexpression of native genes, enabled the addition of sequences encoding secretion …
A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding
S Mukherjee, MD Retwitzer, SM Hubbell… - Briefings in …, 2023 - academic.oup.com
Riboswitches are conserved structural ribonucleic acid (RNA) sensors that are mainly found
to regulate a large number of genes/operons in bacteria. Presently,> 50 bacterial riboswitch …
to regulate a large number of genes/operons in bacteria. Presently,> 50 bacterial riboswitch …
Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the
expression of the associated genes involved in biosynthesis or transport of the …
expression of the associated genes involved in biosynthesis or transport of the …
incaRNAfbinv: a web server for the fragment-based design of RNA sequences
In recent years, new methods for computational RNA design have been developed and
applied to various problems in synthetic biology and nanotechnology. Lately, there is …
applied to various problems in synthetic biology and nanotechnology. Lately, there is …
Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria
Riboswitches are cis-regulatory elements that regulate the expression of genes involved in
biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of …
biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of …
[HTML][HTML] The Bacillaceae-1 RNA motif comprises two distinct classes
E González-Tortuero, C Anthon, JH Havgaard… - Gene, 2022 - Elsevier
Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted
non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 …
non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 …
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs
RNA design has conceptually evolved from the inverse RNA folding problem. In the classical
inverse RNA problem, the user inputs an RNA secondary structure and receives an output …
inverse RNA problem, the user inputs an RNA secondary structure and receives an output …