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Structural motif discovery software tools | RNA data analysis

Motif discovery is the problem of finding recurring patterns in biological data. Patterns can be sequential, mainly when discovered in DNA sequences. They can also be structural (e.g. when discovering RNA motifs). Finding common structural patterns…
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TEISER
Desktop

TEISER Tool for Eliciting Informative Structural Elements in RNA

Allows users to identify the structural motifs that are informative of…

Allows users to identify the structural motifs that are informative of whole-genome measurements across all the transcripts. TEISER employs mutual information to measure the regulatory consequences…

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JAR3D
Web
Desktop

JAR3D Java-based Alignment of RNA using 3D structure

Identifies possible 3D geometries of user-provided hairpin (HL) and internal…

Identifies possible 3D geometries of user-provided hairpin (HL) and internal (IL) loop sequences from predicted RNA 2D structures. JAR3D is a web app that scores sequences to motif groups based on…

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CMfinder
Desktop
Web

CMfinder

A tool to predict RNA motifs. It is an expectation maximization algorithm using…

A tool to predict RNA motifs. It is an expectation maximization algorithm using covariance models for motif description, carefully crafted heuristics for effective motif search, and a novel Bayesian…

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MONSTER
Desktop

MONSTER

Enables users to detect structural motifs shared between two RNAs. MONSTER is…

Enables users to detect structural motifs shared between two RNAs. MONSTER is composed of two main core modules (i) to assign a unique structure to the reference RNA encoded by a set of Non Branching…

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RNAProfile
Desktop

RNAProfile

Uses a heuristic to extract a set of candidate regions from each sequence. The…

Uses a heuristic to extract a set of candidate regions from each sequence. The second step involves grouping regions to find similar motifs. RNAProfile takes as input a set of unaligned RNA sequences…

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Structurexplor
Web

Structurexplor

Furnishes a web-based tool platform to enable the exploration process for RNA…

Furnishes a web-based tool platform to enable the exploration process for RNA secondary structures. Structurexplor generates clusters and structure hierarchies and provides information about the most…

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FOLDALIGN
Desktop
Web

FOLDALIGN

An algorithm for local or global simultaneous folding and aligning two or more…

An algorithm for local or global simultaneous folding and aligning two or more RNA sequences and is based on the Sankoffs algorithm. Foldalign can make pairwise local or global alignments and…

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TSDD
Web

TSDD Transcript Structure and Domain Display

A publicly available, web-based program that provides publication quality…

A publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD relies on GFF/GFF3 files to draw the transcript structures and domains.…

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hts-exploration
Desktop

hts-exploration

Analyzes in vitro selection data for RNA-protein interactions that may…

Analyzes in vitro selection data for RNA-protein interactions that may primarily rely on specific local features in the context of a larger secondary structure. hts-exploration is a Clojure library…

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profiling
Desktop

profiling RNAStructProfiling

Uses GTBoltzmann to sample 1,000 structures, which it then processes into helix…

Uses GTBoltzmann to sample 1,000 structures, which it then processes into helix classes and profiles. Such a combinatorial view of the 1,000 structures allows for structural signal to emerge from the…

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NoFold
Desktop

NoFold

Generates and automatically extracts cohesive clusters, which can be used to…

Generates and automatically extracts cohesive clusters, which can be used to find structure motifs in RNA sequences. NoFold compares the studied files against the 1973 Rfam covariance models (CMs),…

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RNAMotifScanX
Desktop

RNAMotifScanX

A motif search tool based on a base-interaction graph alignment algorithm. This…

A motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX…

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RNAMotifScan
Desktop

RNAMotifScan

A RNA structural alignment method for RNA structural motif identification which…

A RNA structural alignment method for RNA structural motif identification which takes into consideration the isosteric (both canonical and non-canonical) base pairs and multi-pairings in RNA…

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RLooM
Dataset

RLooM

Allows the insertion and replacement of loop structures of a desired sequence…

Allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. RLooM is a comprehensive database of loops in RNA structures can be accessed through the…

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GraphClust
Desktop

GraphClust

Compars and clusters RNAs according to sequence and structure. GraphClust…

Compars and clusters RNAs according to sequence and structure. GraphClust scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against…

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SCARNA_LM
Desktop

SCARNA_LM SCARNA Local Multiple

A pairwise local alignment model and local multiple alignment method for the…

A pairwise local alignment model and local multiple alignment method for the detection of conserved ncRNAs from unaligned sequences. SCARNA_LM uses a local multiple alignment construction procedure…

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Locomotif
Desktop

Locomotif

A GUI-based program that allows for the visual design of RNA motifs. The…

A GUI-based program that allows for the visual design of RNA motifs. The graphical structures are then translated into executable programs to be used for searching a motif in a sequence (plain text…

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comRNA
Desktop

comRNA

A method for predicting common RNA secondary structure motifs in a set of…

A method for predicting common RNA secondary structure motifs in a set of functionally or evolutionarily related RNA sequences. comRNA is based on comparison of stems (palindromic helices) between…

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RNAmine
Web

RNAmine

Employs a graph theoretic representation of RNA sequences and detects all the…

Employs a graph theoretic representation of RNA sequences and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently…

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RNApromo
Web

RNApromo

An efficient computational tool for identifying structural elements within…

An efficient computational tool for identifying structural elements within mRNAs that are involved in specifying posttranscriptional regulations. RNApromo reveals unexplored layers of…

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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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Seed
Desktop

Seed

An algorithm to identify all the conserved RNA secondary structure motifs in a…

An algorithm to identify all the conserved RNA secondary structure motifs in a set of unaligned sequences. Seed takes as input a set of unaligned RNA sequences and produces a set of secondary…

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DiscoverR
Desktop

DiscoverR

Detects common patterns of two RNA secondary structures. DiscoverR is a method…

Detects common patterns of two RNA secondary structures. DiscoverR is a method that works by representing RNA secondary structures as ordered labeled trees, and then performs tree pattern discovery…

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GPRM
Web

GPRM

A genetic programming approach to finding common secondary structure elements…

A genetic programming approach to finding common secondary structure elements in a set of unaligned coregulated or homologous RNA sequences. GPRM has a flexible RNA secondary structure…

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SLASH
Web

SLASH Stem-Loop Align SearcH

Uses FOLDALIGN to find local alignments in RNA sequences. Then COVE to build a…

Uses FOLDALIGN to find local alignments in RNA sequences. Then COVE to build a SCFG model from the local alignments.

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