4.8 Article

R2DT is a framework for predicting and visualising RNA secondary structure using templates

Related references

Note: Only part of the references are listed.
Review Biochemical Research Methods

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Franziska Hufsky et al.

Summary: This review explores bioinformatics workflows and tools for the detection, analysis, tracking, evaluation, research, detection of drug targets, and development of therapeutic strategies related to SARS-CoV-2, providing valuable insights for the ongoing COVID-19 pandemic.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemical Research Methods

RNApuzzler: efficient outerplanar drawing of RNA-secondary structures

Daniel Wiegreffe et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

The EMBL-EBI search and sequence analysis tools APIs in 2019

Fabio Madeira et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs

Boris Shabash et al.

PLOS ONE (2019)

Article Biochemistry & Molecular Biology

RNAcentral: a hub of information for non-coding RNA sequences

Blake A. Sweeney et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

FlyBase 2.0: the next generation

Jim Thurmond et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Mathematical & Computational Biology

rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots

Jan Jelinek et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2019)

Article Biochemistry & Molecular Biology

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

Cynthia L. Smith et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Translation: The Universal Structural Core of Life

Chad R. Bernier et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemical Research Methods

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

Elena Rivas et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

Genenames.org: the HGNC and VGNC resources in 2017

Bethan Yates et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

Ingrid M. Keseler et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

RNA Visualization: Relevance and the Current State-of-the-Art Focusing on Pseudoknots

Boris Shabash et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2017)

Article Biochemical Research Methods

TRAVeLer: a tool for template-based RNA secondary structure visualization

Richard Elias et al.

BMC BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

Peter Kerpedjiev et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

PomBase 2015: updates to the fission yeast database

Mark D. McDowall et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

Drawing and Editing the Secondary Structure(s) of RNA

Yann Ponty et al.

RNA BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

Secondary Structures of rRNAs from All Three Domains of Life

Anton S. Petrov et al.

PLOS ONE (2014)

Article Biochemical Research Methods

nhmmer: DNA homology search with profile HMMs

Travis J. Wheeler et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

dictyBase 2013: integrating multiple Dictyostelid species

Siddhartha Basu et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

Secondary structure and domain architecture of the 23S and 5S rRNAs

Anton S. Petrov et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

WormBase 2012: more genomes, more data, new website

Karen Yook et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Saccharomyces Genome Database: the genomics resource of budding yeast

J. Michael Cherry et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

R-chie: a web server and R package for visualizing RNA secondary structures

Daniel Lai et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

R2R-software to speed the depiction of aesthetic consensus RNA secondary structures

Zasha Weinberg et al.

BMC BIOINFORMATICS (2011)

Article Cell Biology

Predicting and Modeling RNA Architecture

Eric Westhof et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2011)

Article Biochemical Research Methods

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

VARNA: Interactive drawing and editing of the RNA secondary structure

Kevin Darty et al.

BIOINFORMATICS (2009)

Article Biology

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

Michael Sarver et al.

JOURNAL OF MATHEMATICAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures

Yanga Byun et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Tools for the automatic identification and classification of RNA base pairs

HW Yang et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemical Research Methods

The Protein Data Bank

HM Berman et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2002)

Article Biochemistry & Molecular Biology

The accuracy of ribosomal RNA comparative structure models

RR Gutell et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2002)