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Sequence-structure pattern search software tools | RNA data analysis

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted…
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RAG-3D
Web

RAG-3D

A dataset of RNA tertiary (3D) structures and substructures plus a web-based…

A dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural…

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RNAPattMatch
Desktop
Web

RNAPattMatch

Searching for RNA sequence-structure patterns is becoming an essential tool for…

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries…

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Bcheck
Desktop

Bcheck

Performs efficient RNase P RNA gene prediction. Bcheck employs sensitive…

Performs efficient RNase P RNA gene prediction. Bcheck employs sensitive descriptor model (DM) that acts as a filter and a derivation of a sensitive statistics covariance model (CM). It uses…

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iDeepS
Desktop

iDeepS

Infers both sequence and structure preferences of RNA-binding proteins (RBPs).…

Infers both sequence and structure preferences of RNA-binding proteins (RBPs). iDeepS is a deep learning method which consists of convolutional neural networks (CNNs) and a Bidirectional Long Short…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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R3D-BLAST
Web

R3D-BLAST

A BLAST-like search tool that allows the user to quickly and accurately search…

A BLAST-like search tool that allows the user to quickly and accurately search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. The basic idea…

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FASTR3D
Web

FASTR3D Fast and Accurate Search Tool for RNA 3D Structures

A web-based search tool that allows the user to fast and accurately search the…

A web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, FASTR3D allows the user to input three types of queries: (i) a…

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PatSearch
Web

PatSearch

A flexible and fast pattern matcher able to search for specific combinations of…

A flexible and fast pattern matcher able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices. It can also allow for…

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RNAMotif
Desktop

RNAMotif

Searches a database for RNA sequences that match a "motif" describing…

Searches a database for RNA sequences that match a "motif" describing secondary structure interactions. A match means that the given sequence is capable of adopting the given secondary…

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RNAMST
Web

RNAMST

An efficient and flexible RNA motif search tool for RNA structural homologs.…

An efficient and flexible RNA motif search tool for RNA structural homologs. RNAMST web server accepts four different kinds of input formats to facilitate user to describe a RNA structure easily.…

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DARN
Web
Desktop

DARN

Finds new occurrences of characterized non-coding RNAs. DARN is a software tool…

Finds new occurrences of characterized non-coding RNAs. DARN is a software tool for ncRNA localization, which, compared to existing pattern-matching based tools, offers additional expressivity (such…

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RaligNAtor
Desktop

RaligNAtor

Provides index-based and online algorithms for fast approximate matching of RNA…

Provides index-based and online algorithms for fast approximate matching of RNA sequence structure patterns. RaligNAtor is a package that supports a full set of edit operations on single bases and…

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ARNold
Web

ARNold

Combines two published prediction algorithms, Erpin and RNAmotif, and performs…

Combines two published prediction algorithms, Erpin and RNAmotif, and performs nearly as well as more complex procedures while being accessible to the non-specialist. ARNold is a web server that…

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RNABOB
Desktop

RNABOB

Structure-based searches are increasingly used to discover known RNA motifs in…

Structure-based searches are increasingly used to discover known RNA motifs in sequence databases. RNABOB performs such searches by allowing the user to define a desired motif's sequence, paired…

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Structator
Desktop

Structator

A method and readily applicable software tool for time efficient matching of…

A method and readily applicable software tool for time efficient matching of RNA sequence-structure patterns in sequence databases. The presented method's sublinear expected running time makes…

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StemSearch
Web
Desktop

StemSearch

Searches for RNA homologues in a genomic sequence. StemSearch uses an…

Searches for RNA homologues in a genomic sequence. StemSearch uses an inverted-index based sequence-structure RNA search engine. It is based on identifying potential stems in genomic sequences and…

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