BRIO: a web server for RNA sequence and structure motif scan.
Ontology highlight
ABSTRACT:
SUBMITTER: Guarracino A
PROVIDER: S-EPMC8262756 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Motivation:RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. Results:The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. Availability and implementation:The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. Contact:marco.pietrosanto@uniroma2.it. Supplementary information:Supplementary data are available at Bioinformatics online.
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Project description:Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relationships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) information. Sequences and 3D structures contain non-overlapping sets of information that both determine RNA functions. When comparing RNA 3D structures, both types of information need to be taken into account. However, few methods compare RNA structures using both sequence and 3D structure information. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to research community. The web server is located at http://cloud.stat.fsu.edu/RASS/.
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Project description:The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n(2)) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter.
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Project description:BackgroundUnderstanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm.ResultsIn this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated.ConclusionTo the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
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Project description:The BaMM web server offers four tools: (i) de-novo discovery of enriched motifs in a set of nucleotide sequences, (ii) scanning a set of nucleotide sequences with motifs to find motif occurrences, (iii) searching with an input motif for similar motifs in our BaMM database with motifs for >1000 transcription factors, trained from the GTRD ChIP-seq database and (iv) browsing and keyword searching the motif database. In contrast to most other servers, we represent sequence motifs not by position weight matrices (PWMs) but by Bayesian Markov Models (BaMMs) of order 4, which we showed previously to perform substantially better in ROC analyses than PWMs or first order models. To address the inadequacy of P- and E-values as measures of motif quality, we introduce the AvRec score, the average recall over the TP-to-FP ratio between 1 and 100. The BaMM server is freely accessible without registration at https://bammmotif.mpibpc.mpg.de.
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Project description:The CENTROIDFOLD web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple. You can paste a single RNA sequence (FASTA or plain sequence text) or a multiple alignment (CLUSTAL-W format) into the textarea then click on the 'execute CentroidFold' button. The server quickly responses with a prediction result. The major advantage of this server is that it employs our original CentroidFold software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement.
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Project description:Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of foldalign. The server can be used to scan two sequences for a common structural RNA motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. The web server can be accessed at http://foldalign.kvl.dk.
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Project description:Prediction of RNA secondary structure is important in the functional analysis of RNA molecules. The RDfolder web server described in this paper provides two methods for prediction of RNA secondary structure: random stacking of helical regions and helical regions distribution. The random stacking method predicts secondary structure by Monte Carlo simulations. The method of helical regions distribution predicts secondary structure based on the helices that appear most frequently in the set of structures, which are generated by the random stacking method. The RDfolder web server can be accessed at http://rna.cbi.pku.edu.cn.
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Project description:Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/.
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