Recent developments in the MAFFT multiple sequence alignment program

K Katoh, H Toh - Briefings in bioinformatics, 2008 - academic.oup.com
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins
have long been and are still important issues in bioinformatics. To rapidly construct a …

Multiple sequence alignment modeling: methods and applications

M Chatzou, C Magis, JM Chang… - Briefings in …, 2016 - academic.oup.com
This review provides an overview on the development of Multiple sequence alignment
(MSA) methods and their main applications. It is focused on progress made over the past …

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

I Kalvari, EP Nawrocki… - Nucleic Acids …, 2021 - academic.oup.com
Rfam is a database of RNA families where each of the 3444 families is represented by a
multiple sequence alignment of known RNA sequences and a covariance model that can be …

ViennaRNA Package 2.0

R Lorenz, SH Bernhart… - Algorithms for molecular …, 2011 - Springer
Background Secondary structure forms an important intermediate level of description of
nucleic acids that encapsulates the dominating part of the folding energy, is often well …

The vienna RNA websuite

AR Gruber, R Lorenz, SH Bernhart… - Nucleic acids …, 2008 - academic.oup.com
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 …

Phage anti-CRISPR control by an RNA-and DNA-binding helix–turn–helix protein

N Birkholz, K Kamata, M Feussner, ME Wilkinson… - Nature, 2024 - nature.com
In all organisms, regulation of gene expression must be adjusted to meet cellular
requirements and frequently involves helix–turn–helix (HTH) domain proteins. For instance …

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs

S Will, T Joshi, IL Hofacker, PF Stadler, R Backofen - Rna, 2012 - rnajournal.cshlp.org
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 …

RNAalifold: improved consensus structure prediction for RNA alignments

SH Bernhart, IL Hofacker, S Will, AR Gruber… - BMC …, 2008 - Springer
Background The prediction of a consensus structure for a set of related RNAs is an important
first step for subsequent analyses. RNAalifold, which computes the minimum energy …

GraphProt: modeling binding preferences of RNA-binding proteins

D Maticzka, SJ Lange, F Costa, R Backofen - Genome biology, 2014 - Springer
We present GraphProt, a computational framework for learning sequence-and structure-
binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental …

Metazoan tRNA introns generate stable circular RNAs in vivo

Z Lu, GS Filonov, JJ Noto, CA Schmidt, TL Hatkevich… - Rna, 2015 - rnajournal.cshlp.org
We report the discovery of a class of abundant circular noncoding RNAs that are produced
during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric) RNAs …