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 …

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 …

Abstract Background Structural alignment of RNAs is becoming important, since the
discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on …

Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining
the concept of ribosomal constraints on rRNA genes; the degree of variation is an important …

RNA secondary structures have proven essential for understanding the regulatory functions
performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success …

We present a continuous benchmarking approach for the assessment of RNA secondary
structure prediction methods implemented in the CompaRNA web server. As of 3 October …

With the dramatic increase in RNA 3D structure determination in recent years, we now know
that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has …

Background Aligning multiple RNA sequences is essential for analyzing non-coding RNAs.
Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for …

R-Coffee is a multiple RNA alignment package, derived from T-Coffee, designed to align
RNA sequences while exploiting secondary structure information. R-Coffee uses an …

RNA biology has risen to prominence after a remarkable discovery of diverse functions of
noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions …