SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

Tommaso, Paolo Di; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cédric

doi:10.1093/nar/gku459

Cited by 3 publications

(2 citation statements)

References 24 publications

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“…Corresponding sequence and secondary structures information were also taken from the PDB files and analyzed with 3DNA software suite 34 . TPPsw ec and TPPsw at sequences were then aligned using the SARA-Coffee mode of T-Coffee program 35 , and figures of sequence alignment were rendered using ALINE 36 . The secondary structure calculated on the basis of the PDB files of the crystallographic structures was compared through the SimTree server 20 .…”

Section: Methodsmentioning

confidence: 99%

Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

Antunes

Jorge

Costa

et al. 2019

Sci Rep

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Riboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat. TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.

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Section: Methodsmentioning

confidence: 99%

Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

Antunes

Jorge

Costa

et al. 2019

Sci Rep

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“…The required secondary structure information is provided by an external program, 3DNA ( 12 ). SARA-Coffee is the enhancement of SARA, combining its algorithm with R-Coffee ( 13 ) to produce multiple-sequence alignments using both sequence and structural data ( 14 ). LaJolla uses an n-gram model to generate hash tables for analyzing similar derived sequence ( 15 ).…”

Section: Introductionmentioning

confidence: 99%

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments

Piątkowski

Jabłońska

Żyła

et al. 2017

Nucleic Acids Research

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RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures. Here, we present SupeRNAlign (v1.3.1), a new method for flexible superposition of RNA 3D structures, and SupeRNAlign-Coffee—a workflow that combines SupeRNAlign with T-Coffee for inferring structure-based sequence alignments. The methods have been benchmarked with eight other methods for RNA structural superposition and alignment. The benchmark included 151 structures from 32 RNA families (with a total of 1734 pairwise superpositions). The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database. SupeRNAlign and SupeRNAlign-Coffee achieved significantly higher scores than most of the benchmarked methods: SupeRNAlign generated the most accurate sequence alignments among the structure superposition methods, and SupeRNAlign-Coffee performed best among the sequence alignment methods.

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Identification and characterization of two selenium-dependent glutathione peroxidase 1 isoforms from Larimichthys crocea

Xie

Chen

Zhu

2017

Fish & Shellfish Immunology

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SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

Cited by 3 publications

References 24 publications

Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments

Identification and characterization of two selenium-dependent glutathione peroxidase 1 isoforms from Larimichthys crocea

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