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Structure alignment software tools | RNA data analysis

The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and…
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RMfam
Desktop

RMfam RNA Motif Families

A database of annotated multiple sequence alignments and probabilistic models…

A database of annotated multiple sequence alignments and probabilistic models for a number of RNA motifs. RMfam presents 34 alignments, consensus structures and corresponding probabilistic models of…

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WebSTAR3D
Web

WebSTAR3D

A user-friendly online interface for the alignment of RNA 3D structures.…

A user-friendly online interface for the alignment of RNA 3D structures. WebSTAR3D globally aligns RNA structures with a two-step strategy: first, it finds the consensus of stacks between the…

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CRAST
Desktop

CRAST Context RNA Alignment Search Tool

CRAST is a non-coding RNAs (ncRNA) alignment tool based on LAST. The software…

CRAST is a non-coding RNAs (ncRNA) alignment tool based on LAST. The software provides a BLAST-like RNA alignment search algorithm. The CRAST algorithm pairwises-align numerous ncRNAs with…

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Junction-Explor…
Web

Junction-Explorer

Introduces a computational method to predict, at the secondary structure level,…

Introduces a computational method to predict, at the secondary structure level, the coaxial helical stacking arrangement in junctions, as well as classify the junction topology. Junction-Explorer…

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CARNA
Web

CARNA

Allows multiple alignment of RNA molecules. CARNA does not pick the most likely…

Allows multiple alignment of RNA molecules. CARNA does not pick the most likely consensus structure, but computes the alignment that fits best to all likely structures simultaneously. Hence, CARNA is…

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STAR3D
Desktop

STAR3D

An RNA 3D structural alignment tool to take into full account the 2D relations…

An RNA 3D structural alignment tool to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs…

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SECISaln
Web

SECISaln

Constructs structure-based alignments of an extensive dataset of eukaryotic…

Constructs structure-based alignments of an extensive dataset of eukaryotic SECIS (a stem-loop structure on the 3' UTR of Selenoprotein mRNA transcripts) sequences. SECISaln can be applied on…

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Rclick
Web

Rclick

Aligns pairs of RNA structures. Rclick is a topology independent structure…

Aligns pairs of RNA structures. Rclick is a topology independent structure superimposition program. It can identify local structural similarities of RNA structures and RNA-protein complexes,…

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MXSCARNA
Web

MXSCARNA Multiplex Stem Candidate Aligner for RNAs

A multiple alignment tool for RNA sequences using progressive alignment based…

A multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.

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SARA-Coffee
Web

SARA-Coffee

A service allowing the online computation of 3D structure based multiple RNA…

A service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set…

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RASS
Desktop
Web

RASS RNA alignment in the joint Sequence-Structure space

Provides a tool for users to compare and align two RNA molecules in the joint…

Provides a tool for users to compare and align two RNA molecules in the joint sequence-structure space. The user will provide two RNA molecules as input where one may be a RNA molecule with known…

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CHSalign
Web
Desktop

CHSalign

A method for aligning two RNA secondary (2D) structures that possess coaxial…

A method for aligning two RNA secondary (2D) structures that possess coaxial helical stacking (CHS) motifs within the junctions of the two RNA structures. CHSalign is intended to be an efficient…

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BoulderALE
Desktop

BoulderALE Boulder Alignment Editor

Allows for the annotation of Watson-Crick and non-Watson-Crick basepairs,…

Allows for the annotation of Watson-Crick and non-Watson-Crick basepairs, annotation of features (i.e. stems, loops, etc.), collapsing of features (horizontal) and sequences (vertical), along with 2D…

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PSMAlign
Desktop

PSMAlign Progressive Stem Matching Alignment

An open source tool that performs pairwise RNA secondary structures alignment…

An open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. PSMAlign enables alignment of large structures, such as those in the 23S…

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WAR
Web

WAR Webserver for Aligning non-coding RNAs

Permits the simultaneously use of a number of state of the art methods for…

Permits the simultaneously use of a number of state of the art methods for performing multiple alignment and secondary structure prediction for noncoding RNA sequences. WAR is useful tool for any…

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RNALogo
Web

RNALogo

Presents a graphical representation of the patterns in an aligned RNA sequences…

Presents a graphical representation of the patterns in an aligned RNA sequences with a consensus structure. Several significant features, including sequence conservation, structural conservation, and…

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DIAL
Web

DIAL DIhedral ALignment Server

Provides public access to a dynamic programming algorithm for pairwise 3D…

Provides public access to a dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral…

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iPARTS
Web

iPARTS

An improved web server for aligning two RNA 3D structures based on a structural…

An improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global…

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ARTS
Desktop
Web

ARTS Alignment of RNA Tertiary Structures

A web server built around ARTS, a method for aligning tertiary structures of…

A web server built around ARTS, a method for aligning tertiary structures of nucleic acids (both RNA and DNA). ARTS receives a pair of 3D nucleic acid structures and searches for a priori unknown…

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SARA
Web

SARA

A program for pair-wise alignment of RNA structures as a web server for…

A program for pair-wise alignment of RNA structures as a web server for structure-based RNA function assignment. The SARA server relies on the SARA program, which aligns two RNA structures based on a…

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SETTER
Web

SETTER SEcondary sTructure-based TERtiary Structure Similarity Algorithm

A web server for the RNA structure pairwise comparison utilizing the SETTER…

A web server for the RNA structure pairwise comparison utilizing the SETTER algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called…

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R3D Align
Web
Desktop

R3D Align

Decomposes 3D structure into sets of local nucleotide neighbourhoods, which…

Decomposes 3D structure into sets of local nucleotide neighbourhoods, which typically overlap in the sense that each nucleotide is included in more than one set. R3D Align is a web server that for…

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GR-Align
Desktop

GR-Align GRaphlet-based Aligner

A fast heuristic procedure for aligning/comparing protein structures according…

A fast heuristic procedure for aligning/comparing protein structures according to the Contact Map Overlap maximization (CMO) paradigm. GR-Align is based on a Needleman-Wunch algorithm where the cost…

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MultiSETTER
Web

MultiSETTER

A tool for superposition of multiple RNA structures. It is based on a pairwise…

A tool for superposition of multiple RNA structures. It is based on a pairwise RNA superposition algorithm called SETTER. The main idea of MultiSETTER is to build an average structure and to…

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Gardenia
Web
Desktop

Gardenia

A theoretical unifying framework for comparing arc-annotated sequences.…

A theoretical unifying framework for comparing arc-annotated sequences. Gardenia takes into account both the primary structure and the secondary structure to build an accurate multiple alignment. It…

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PMcomp /…
Desktop

PMcomp / PMmulti

Performs pairwise and progressive multiple alignments of RNA sequences. PMcomp…

Performs pairwise and progressive multiple alignments of RNA sequences. PMcomp is a variant of Sankoff's algorithm for simultaneous folding and alignment, which takes as input pre-computed base…

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DAFS
Desktop

DAFS

Simultaneously aligns and folds RNA sequences based on maximizing expected…

Simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment. DAFS decomposes the pairwise structural alignment…

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StrAl
Web
Desktop

StrAl

Provides multiple alignments of non-coding RNAs following a fast progressive…

Provides multiple alignments of non-coding RNAs following a fast progressive strategy. StrAl combines the thermodynamic base pairing information derived from RNAfold calculations in the form of base…

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Cofolga2mo
Desktop

Cofolga2mo

A structural RNA sequence alignment program on the basis of MOGA. Cofolga2mo is…

A structural RNA sequence alignment program on the basis of MOGA. Cofolga2mo is designed for global pairwise sequence alignment. By performing a BRAliBase 2.1 benchmark test, we found that the…

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RNA-Pareto
Desktop

RNA-Pareto

Allows a direct inspection of all feasible results to the pairwise RNA…

Allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set. RNA-Pareto assists in…

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FRIEs
Desktop

FRIEs Fast RNA structural Identity Estimator

A little tool that gives you structural alignments of RNA coordinate files. It…

A little tool that gives you structural alignments of RNA coordinate files. It is using probabilistic, Bayesian methods to automatically find statistically and structurally distinct and recognizable…

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RSmatch
Desktop

RSmatch

Uses for aligning RNA secondary structures and for motif detection. RSmatch is…

Uses for aligning RNA secondary structures and for motif detection. RSmatch is an efficient tool that can find the optimal global or local alignment between two RNA secondary structures using two…

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ERA
Desktop

ERA

Compares RNA secondary structures. ERA aims at deleting obsolete candidates by…

Compares RNA secondary structures. ERA aims at deleting obsolete candidates by incorporating the sparse dynamic programming technique. ERA can be used to perform all-against-all alignments on these…

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LARA
Desktop

LARA LAgrangian Relaxed Alignments

Employs methods from combinatorial optimization to compute feasible solutions…

Employs methods from combinatorial optimization to compute feasible solutions for an integer linear program. LARA computes all pairwise sequence-structure alignments of the input sequences and passes…

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SISSIz
Desktop

SISSIz

Simulates multiple alignments of a given average dinucleotide content. SISSIz…

Simulates multiple alignments of a given average dinucleotide content. SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get…

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Consan
Desktop

Consan

An implementation of a pairwise stochastic context-free grammar for RNA…

An implementation of a pairwise stochastic context-free grammar for RNA structural alignment. We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework…

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FRASS
Desktop
Web

FRASS

Represents a RNA chain with its Gauss integrals and allows one to compare…

Represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. The FRASS web-server…

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PMFastR
Desktop

PMFastR

Implements an algorithm which iteratively uses a sequence-structure alignment…

Implements an algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment. PMFastR has low memory consumption allowing for the alignment of…

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RNA-TVcurve
Web

RNA-TVcurve

Delivers a suite of RNA analysis functions for inferring RNAs’ relationship…

Delivers a suite of RNA analysis functions for inferring RNAs’ relationship based on comparing their secondary-structures. Functions include i) visualization of numerical representation of RNA…

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Murlet
Web

Murlet

A multiple alignment tool for RNA sequences using iterative alignment based on…

A multiple alignment tool for RNA sequences using iterative alignment based on Sankoff's algorithm with sharply reduced computational time.

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Web-Beagle
Web

Web-Beagle Web-BEar Alignment Globla and Local

A web server for the pairwise global or local alignment of RNA secondary…

A web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural…

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ESA
Desktop

ESA Elastic Shape Analysis

An RNA alignment method based on elastic shape analysis. ESA treats RNA…

An RNA alignment method based on elastic shape analysis. ESA treats RNA structures as three dimensional curves with sequence information encoded on additional dimensions so that the alignment can be…

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SARSA
Web

SARSA

A web tool that can be used to align two or more RNA tertiary structures. In…

A web tool that can be used to align two or more RNA tertiary structures. In SARSA, two RNA structural alignment tools are provided: 1) PARTS for pairwise alignment of RNA tertiary structures and 2)…

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CentroidAlign-W…
Web

CentroidAlign-Web

A web server for aligning multiple RNA sequences by extending CentroidAlign,…

A web server for aligning multiple RNA sequences by extending CentroidAlign, which is a fast and accurate multiple aligner for RNA sequences that considers secondary structures. We showed that…

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RNASAlign
Desktop

RNASAlign

Automatically identifies the pseudoknot type of a secondary structure and…

Automatically identifies the pseudoknot type of a secondary structure and perform structural alignment of a folded RNA with every region of a target DNA/RNA sequence. RNASAlign reports to the user…

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BlockMatch
Web
Desktop

BlockMatch

Alignes two blocks, where a block is an RNA multiple sequence alignment with…

Alignes two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. BlockMatch employs a quadratic-time dynamic…

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