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Protein-RNA interaction analysis (omic data)

Interactions between proteins and RNA play essential roles for life. For example, protein-RNA interactions mediate RNA metabolic processes such as splicing, polyadenylation, messenger RNA stability, localization and translation (Tuschl, 2003).…
HADDOCK
Web

HADDOCK High Ambiguity Driven protein-protein DOCKing

An information-driven flexible docking approach for the modeling of…

An information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from…

Global Score
Web

Global Score

Predicts protein interactions with transcripts > 1000nt. Global Score is an…

Predicts protein interactions with transcripts > 1000nt. Global Score is an algorithm that integrates the information coming from protein and RNA fragments into an overall binding propensity…

NPIDB
Dataset

NPIDB Nucleic Acids—Protein Interaction DataBase

Provides an access to information about all available structures of DNA–protein…

Provides an access to information about all available structures of DNA–protein and RNA–protein complexes. The NPIDB database contains comparative structural information on some SCOP families. It…

RESA
Desktop

RESA RNA Element Selection Assay

Provides a quantitative measurement of RNA elements regulatory functions at…

Provides a quantitative measurement of RNA elements regulatory functions at near-nucleotide resolution. RESA selects RNA elements on the basis of their activity in vivo and uses high-throughput…

RBNS
Desktop

RBNS RNA Bind-n-seq

Characterizes sequence and structural specificity of RNA binding proteins…

Characterizes sequence and structural specificity of RNA binding proteins (RBPs) RBNS is a method which allows to measure the binding affinity of proteins for specific RNA sequences. The software…

PatchDock
Web
Desktop

PatchDock

Finds docking transformations that yield good molecular shape complementarity.…

Finds docking transformations that yield good molecular shape complementarity. A wide interface is ensured to include several matched local features of the docked molecules. PatchDock divides the…

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NPInter
Dataset

NPInter Noncoding RNAs and Protein related biomacromolecules Interaction

Catalogs experimentally determined functional interactions between ncRNAs and…

Catalogs experimentally determined functional interactions between ncRNAs and proteins, mRNAs or genomic DNA sequences. NPInter integrates the diverse body of experimental knowledge about functional…

ProNIT
Dataset

ProNIT

Provides experimentally determined thermodynamic interaction data between…

Provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. ProNIT is useful for researchers wishing to study the underlying mechanisms of protein stability…

NDB
Dataset

NDB Nucleic Acid Database

Performs searches based on annotations relating to sequence, structure and…

Performs searches based on annotations relating to sequence, structure and function. The Nucleic Acid Database is a web portal that provides access to information about 3D nucleic acid structures and…

BindUP
Web

BindUP

Predicts DNA and RNA binding proteins using a non-homology-based approach.…

Predicts DNA and RNA binding proteins using a non-homology-based approach. BindUP is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP…

TCP-seq
Desktop

TCP-seq translation complex profile sequencing

Uses fast covalent fixation of translation complexes in live cells, followed by…

Uses fast covalent fixation of translation complexes in live cells, followed by RNase footprinting of translation intermediates and their separation into complexes involving either the full ribosome…

DRNApred
Web

DRNApred

Predicts the DNA- and RNA-binding proteins. DRNApred is a webserver that…

Predicts the DNA- and RNA-binding proteins. DRNApred is a webserver that accurately and in high-throughput predicts protein–RNA and protein–DNA binding residues from protein sequences. DRNApred…

3dRPC
Web

3dRPC

Allows users to automatically detect 3D RNA-protein complex structures. 3dRPC…

Allows users to automatically detect 3D RNA-protein complex structures. 3dRPC is a web application that furnishes an interface including two different scoring functions. Users can submit…

PRIDB
Dataset

PRIDB Protein-RNA Interface Database

A comprehensive collection of all protein-RNA complexes from the Protein Data…

A comprehensive collection of all protein-RNA complexes from the Protein Data Bank (PDB).

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catRAPID omics
Web

catRAPID omics

A server for large-scale calculations of protein-RNA interactions. catRAPID…

A server for large-scale calculations of protein-RNA interactions. catRAPID omics allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size…

HotSPRing
Web

HotSPRing Hot Spot at Protein-RNA interacing surface

A web server to predict the host spots in RNA binding proteins (RBPs). The…

A web server to predict the host spots in RNA binding proteins (RBPs). The method for hot spot prediction could be effectively used to narrow down the target residues for inhibiting protein–RNA…

RsiteDB
Dataset

RsiteDB

A database and an on-line search engine, which store and query the protein…

A database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases.

APRICOT
Desktop

APRICOT

Permits sequence-based identification and characterization of protein classes.…

Permits sequence-based identification and characterization of protein classes. APRICOT is a computational pipeline which identifies functional motifs in protein sequences using Position Specific…

omiXcore
Web

omiXcore

Predicts RNA-binding proteins (RBP) interactions with large RNAs. omiXcore…

Predicts RNA-binding proteins (RBP) interactions with large RNAs. omiXcore permits to identify RNA binding sites thanks to local evaluation of physicochemical properties of polypeptide and nucleotide…

PRIdictor
Web

PRIdictor Protein-RNA Interaction preDICTOR

Predicts mutual binding sites in RNA and protein at the nucleotide level…

Predicts mutual binding sites in RNA and protein at the nucleotide level resolutions. PRIdictor is based on the library for support vector machine (SVM) with the radial basis function (RBF) as a…

BIPA
Dataset

BIPA Biological Interaction database for Protein-nucleic Acid

Stores protein-nucleic acid interaction. BIPA is a database that provides…

Stores protein-nucleic acid interaction. BIPA is a database that provides various features of protein–nucleic acid interfaces and non-redundant multiple structural alignments for nucleic acid-binding…

RBscore
Web

RBscore RNA Binding score

A general binding score for predicting the nucleic acid binding probability in…

A general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue…

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RNAmap2D
Desktop

RNAmap2D

Calculates and visualizes nucleic acid contact and distance maps. RNAmap2D…

Calculates and visualizes nucleic acid contact and distance maps. RNAmap2D intends to improve analyzes of RNA structures which focus on type and location of short-range interactions, without taking…

RBDmap
Desktop

RBDmap

Offers a method for identifying RNA-binding domains (RBDs). RBDmap is a…

Offers a method for identifying RNA-binding domains (RBDs). RBDmap is a standalone software that can be used on several cell types and organisms such as S. cerevisiae or Drosophila melanogaster to…

PDBparam
Web

PDBparam

Computes more than 50 structure-based features for any given protein structure.…

Computes more than 50 structure-based features for any given protein structure. PDBparam can deal with inter residue interactions, amino acid propensities, physicochemical properties, and binding…

LPI-ETSLP
Algorithm

LPI-ETSLP LPI eigenvalue transformation-based semi-supervised link prediction

Predicts lncRNA-protein interaction. LPI-ETSLP integrates lncRNA-lncRNA…

Predicts lncRNA-protein interaction. LPI-ETSLP integrates lncRNA-lncRNA similarity network and protein-protein similarity network to predict potential lncRNA-protein interactions. This method is…

NPDock
Web

NPDock Nucleic acid-Protein Dock

A web server for modeling of RNA-protein and DNA-protein complex structures.…

A web server for modeling of RNA-protein and DNA-protein complex structures. NPDock combines (1) GRAMM for global macromolecular docking, (2) scoring with a statistical potential, (3) clustering of…

RBPPred
Desktop

RBPPred

Predicts whether a protein binds RNAs, based on the support vector machine…

Predicts whether a protein binds RNAs, based on the support vector machine (SVM) and on a comprehensive feature representation. By integrating the physicochemical properties with the evolutionary…

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RNAcommender
Desktop

RNAcommender

A tool for genome-wide recommendation of RNA-protein interactions. RNAcommender…

A tool for genome-wide recommendation of RNA-protein interactions. RNAcommender is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the…

catRAPID…
Web

catRAPID signature

Predicts ribonucleoproteins and RNA-binding regions using physico-chemical…

Predicts ribonucleoproteins and RNA-binding regions using physico-chemical properties instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms,…

PRNAclass
Desktop

PRNAclass

A protein local structure multiple alignment algorithm to identify the main…

A protein local structure multiple alignment algorithm to identify the main groups of protein-RNA binding pockets. PRNAclass identifies the structure motifs of protein-RNA binding sites in the form…

DORAEMON
Desktop
Oli
Desktop

Oli

Represents three methods allowing the description of RNA sequences. Oli is the…

Represents three methods allowing the description of RNA sequences. Oli is the first method and uses tetranucleotides as features. OliMo is the second, and integrates motif scores from…

ContPro
Web

ContPro

Calculates amino acid contact distances in proteins at different distance…

Calculates amino acid contact distances in proteins at different distance threshold from the 3 Dimensional (3D)-structure of the protein. ContPro calculates the distance between selected protein…

MORDOR
Desktop

MORDOR MOlecular Recognition with a Driven dynamics OptimizeR

Allows creation of binding site and docking. MORDOR is a software which…

Allows creation of binding site and docking. MORDOR is a software which contains all of the tools for virtual screening. The software can perform the main docking using its own energetic and…

CircInteractome
Web

CircInteractome

A web tool for mapping RBP- and miRNA-binding sites on human circRNAs.…

A web tool for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs…

iONMF
Desktop

iONMF integrative Orthogonality-regularized Nonnegative Matrix Factorization

Integrates multiple data sources and discover non-overlapping, class-specific…

Integrates multiple data sources and discover non-overlapping, class-specific RNA binding patterns of varying strengths. The orthogonality constraint halves the effective size of the factor model and…

PDIdb
Dataset

PDIdb Protein-DNA Interface database

A repository containing relevant structural information of Protein-DNA…

A repository containing relevant structural information of Protein-DNA complexes solved by X-Ray cristallography and available at the Protein Data Bank (PDB).

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RNA Bricks
Dataset

RNA Bricks

Stores information about recurrent RNA 3D motifs and their interactions, found…

Stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA-protein complexes. Besides, the search utility enables searching…

FastRNABindR
Web

FastRNABindR

Predicts protein-RNA interface residues. FastRNABindR does not restrict the…

Predicts protein-RNA interface residues. FastRNABindR does not restrict the number of proteins to submit. It accepts up to 500 proteins per submission and returns prediction results within…

Deep-RBPPred
Desktop

Deep-RBPPred

Predicts RNA binding proteins (RBPs). Deep-RBPPred is based on a deep…

Predicts RNA binding proteins (RBPs). Deep-RBPPred is based on a deep convolutional neural network (CNN) that uses an RBP predicting model. It can minimize final loss function which is consisted of…

PLPIHS
Algorithm

PLPIHS

Predicts IncRNA-Protein Interactions using HeteSims Scores. PLPIHS is an…

Predicts IncRNA-Protein Interactions using HeteSims Scores. PLPIHS is an effective computational method which have been compared to PRINCE, RWR and LPIHN and seems show an AUC score significantly…

RNApin
Desktop

RNApin

Predicts protein interacting nucleotides (PINs). RNApin is a web app providing…

Predicts protein interacting nucleotides (PINs). RNApin is a web app providing prediction results by calculating probability score for each nucleotide of the given RNA sequence. It could be useful…

RPI-Bind
Desktop

RPI-Bind

Identifies the binding sites on a given pair of protein and RNA. RPI-Bind is a…

Identifies the binding sites on a given pair of protein and RNA. RPI-Bind is a three-step method that includes (i) the prediction of RNA binding regions on protein, (ii) the prediction of protein…

LigParGen
Web

LigParGen

Provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force…

Provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field (FF) parameters for organic ligands. LigParGen is a web server which generates ligand parameters for common…

RpveScore
Desktop

RpveScore

Consists of the pairwise potential and six physics-based energy terms.…

Consists of the pairwise potential and six physics-based energy terms. RpveScore is a weighted combined scoring function including physics based energy terms and the knowledge-based pairwise…

Multi-VORFFIP
Web

Multi-VORFFIP

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding…

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding sites. Multi-VORFFIP utilizes a wide range of structural, evolutionary, experimental and energy-based information that…

JET
Desktop

JET Joint Evolutionary Trees

Detects very different types of interactions of a protein with another protein,…

Detects very different types of interactions of a protein with another protein, ligands, DNA, and RNA. JET, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary…

RNABindR
Web

RNABindR

Identifies and displays RNA-binding residues in known protein-RNA complexes and…

Identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown structure. RNABindR uses a distance cutoff to identify which amino…

SPOT-Struct-RNA
Desktop
Web

SPOT-Struct-RNA

RNA-binding Protein Prediction from 3D structure. This method achieves 98%…

RNA-binding Protein Prediction from 3D structure. This method achieves 98% accuracy and 91% precision for predicting RBPs and 93% accuracy and 78% precision for predicting RNA-binding amino-acid…

PRince
Web

PRince Protein-RNA interface

Analyzes the structural features and physicochemical properties of the…

Analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA…

BindN
Web

BindN

Applies support vector machines (SVMs) to prediction of DNA and RNA-binding…

Applies support vector machines (SVMs) to prediction of DNA and RNA-binding residues from sequence features, including the side chain pKa value, hydrophobicity index and molecular mass of an amino…

RStrucFam
Web

RStrucFam

Provides a platform for identifying the RNA-binding protein (RBP) mechanisms.…

Provides a platform for identifying the RNA-binding protein (RBP) mechanisms. RStrucFam is a web application that aims to predict potential structure, functions and RNA partners from a given…

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aRNhAck
Desktop

aRNhAck

Assists users in analyzing non-coding RNA sequences. ARNhAck provides a…

Assists users in analyzing non-coding RNA sequences. ARNhAck provides a software that focuses on the sole biochemical and evolutionary properties of the RNA. It gathers biochemical signal from…

IPMiner
Desktop

IPMiner Interaction Pattern Miner

Predicts ncRNA-protein interactions from protein sequences. IPMiner is based on…

Predicts ncRNA-protein interactions from protein sequences. IPMiner is based on stacked autoencoder. It can automatically learn high-level abstraction features. The tool uses protein sequences to…

rpiCOOL
Desktop

rpiCOOL

Detects RNA–protein interactions. rpiCOOL uses a machine learning method that…

Detects RNA–protein interactions. rpiCOOL uses a machine learning method that uses random forest classifier. It achieves a better performance when there are more data available. The tool classifies…

RBRIdent
Desktop

RBRIdent

A classifier to identify the RNA-binding residues. In an independent benchmark…

A classifier to identify the RNA-binding residues. In an independent benchmark test, RBRIdent achieved an accuracy of 76.79%, Matthews correlation coefficient of 0.3819 and F-measure of 75.58%,…

PRID
Dataset

PRID Protein-RNA Interaction Database

Collects information about protein-RNA interactions (PRIs). PRID provides three…

Collects information about protein-RNA interactions (PRIs). PRID provides three excel files that can be freely downloaded for being browsed: Hydrogen Bonding, Electrostatic Interactions or Stacking…

PRBP
Web

PRBP Prediction of RNA-Binding Proteins

Predicts RNA-binding proteins using the information of predicted RNA-binding…

Predicts RNA-binding proteins using the information of predicted RNA-binding residues in conjunction with a random forest based method. For a given protein, we first predict its RNA-binding residues…

practip
Desktop

practip

A prediction method for residue-base contacts between proteins and RNAs using…

A prediction method for residue-base contacts between proteins and RNAs using only sequence information and structural information predicted from only sequences. practip can be applied to any…

PRIPU
Desktop

PRIPU

Employs biased-support vector machine (SVM) for predicting protein-RNA…

Employs biased-support vector machine (SVM) for predicting protein-RNA interactions (PRIs) using only positive and unlabeled examples. This is the first work that predicts PRIs using only positive…

TeloPIN
Dataset

TeloPIN Telomeric Proteins Interaction Network

A database that points to provide comprehensive information on protein-protein,…

A database that points to provide comprehensive information on protein-protein, protein-DNA and protein-RNA interaction of telomeres. TeloPIN database contains four types of interaction data,…

PRNA
Desktop

PRNA

Identifies the RNA binding sites in proteins by combining interaction…

Identifies the RNA binding sites in proteins by combining interaction propensity with other sequence and structure-based features. PRNA predicts RNA interacting residues in proteins by implementing a…

COCOMAPS
Web

COCOMAPS bioCOmplexes COntact MAPS

A web application to easily and effectively analyse and visualize the interface…

A web application to easily and effectively analyse and visualize the interface in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes), by making use of…

ENTANGLE
Desktop

ENTANGLE

Analyses protein-nucleic acid complexes. ENTANGLE uses available structural…

Analyses protein-nucleic acid complexes. ENTANGLE uses available structural models in their PDB format and searches for appropriate hydrogen bonding, stacking, electrostatic, hydrophobic and van der…

FTDock
Desktop

FTDock Fourier Transform rigid-body Docking

Discretises two molecules onto orthogonal grids and performs a global scan of…

Discretises two molecules onto orthogonal grids and performs a global scan of translational and rotational space. In order to scan rotational space it is necessary to rediscretise one of the…

SPOT-Seq-RNA
Desktop
Web

SPOT-Seq-RNA

A sequence-based technique dedicated for predicting complex structures of…

A sequence-based technique dedicated for predicting complex structures of protein and RNA by combining fold recognition with binding affinity prediction. The method not only provides a highly…

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lncPro
Desktop
Web

lncPro

A web app for predicting the interaction between long noncoding RNAs and…

A web app for predicting the interaction between long noncoding RNAs and proteins. By coding RNA and protein sequences into vectors, a matrix multiplication is used to give score to each RNA-protein…

PTools
Desktop

PTools

Allows users to perform assembly tasks and to simplify developments without…

Allows users to perform assembly tasks and to simplify developments without sacrificing speed for correctness. PTools is able to deal with both coarse-grained as well as atomic resolution…

SRCPred
Web

SRCPred Specific RNA Contact Prediction

Predicts specific RNA-binding sites between the residue environments of…

Predicts specific RNA-binding sites between the residue environments of proteins and dinucleotides in RNA. The SRCPred input is an amino acid sequence in the FASTA format and the output is a set of…

CONS-COCOMAPS
Web

CONS-COCOMAPS CONSensun COCOMAPS

A tool to easily measure and visualize the consensus in multiple docking…

A tool to easily measure and visualize the consensus in multiple docking solutions. It uses the conservation of inter-residue contacts as an estimate of the similarity between different docking…

DBBP
Dataset
OPRA
Web

OPRA Optimal Protein-RNA Area

Predicts RNA-binding areas on proteins. OPRA is able to model protein-RNA…

Predicts RNA-binding areas on proteins. OPRA is able to model protein-RNA interactions of biological and therapeutic interest. It uses statistical information to proceed protein-RNA prediction. The…

Predict_RBP
Desktop

Predict_RBP

Predicts the RNA-binding sites in proteins based on support vector machines…

Predicts the RNA-binding sites in proteins based on support vector machines (SVMs). Predict_RBP is a method incorporated into the prediction of a variety of features from amino acid sequence…

RPISeq
Web

RPISeq

A family of classifiers for predicting RNA-protein interactions using only…

A family of classifiers for predicting RNA-protein interactions using only sequence information. Given the sequences of an RNA and a protein as input, RPIseq predicts whether or not the RNA-protein…

RNAProSite
Web

RNAProSite

We designed two structural features (residue electrostatic surface potential…

We designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the…

PiRaNhA
Web

PiRaNhA Protein-RNA

Predicts the location of RNA-binding residues (RBRs) in protein sequences. The…

Predicts the location of RNA-binding residues (RBRs) in protein sequences. The goal of functional annotation of sequences in the field of RNA binding is to provide predictions of high accuracy that…

SVM-Prot
Web

SVM-Prot

A web app for the prediction of RNA-binding proteins directly from their…

A web app for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding and non-RNA-binding proteins, an SVM system was trained to…

NAPS
Web

NAPS

A method for the identification of amino acid residues involved in DNA- and…

A method for the identification of amino acid residues involved in DNA- and RNA-binding using sequence-based attributes. NAPS used in this work combines the C4.5 algorithm with bootstrap aggregation…

SNBRFinder
Web

SNBRFinder Sequence-based Nucleic acid-Binding Residue Finder

A sequence-based hybrid algorithm for predicting nucleic acid-binding residues.…

A sequence-based hybrid algorithm for predicting nucleic acid-binding residues. To address this problem, the profile HMM alignment was ingeniously utilized to establish the sequence-based template…

RBRDetector
Web

RBRDetector RNA-Binding Residue Detector

A structure-based algorithm to identify RNA-binding residues by combining…

A structure-based algorithm to identify RNA-binding residues by combining feature- and template-based prediction strategies. Based on the well-designed evolutionary and structural features, we…

PRINTR
Web

PRINTR

A method for the prediction of protein residues that interact with RNA using…

A method for the prediction of protein residues that interact with RNA using support vector machine (SVM) and position-specific scoring matrices (PSSMs). Two cases have been considered in the…

POPSCOMP
Web

POPSCOMP

Computes the interaction surface between all components of a given complex…

Computes the interaction surface between all components of a given complex structure consisting of proteins, DNA or RNA molecules. It uses a simple analytical formula with a parameterization designed…

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PRI-Modeler
Desktop

PRI-Modeler protein–RNA interaction modeler

Recognizes the secondary and tertiary structures of RNA. PRI-Modeler analyzes…

Recognizes the secondary and tertiary structures of RNA. PRI-Modeler analyzes the hydrogen bond and van der Waals interactions between protein and RNA from the three-dimensional atomic coordinates of…

RISP
Web

RISP RNA-interaction site prediction

A hybrid RISP method using support vector machine (SVM) in conjunction with…

A hybrid RISP method using support vector machine (SVM) in conjunction with evolutionary information of amino acid sequences in terms of their position-specific scoring matrices (PSSMs) for…

PredRBR
Desktop

PredRBR

Predicts protein-RNA binding sites. PredRBR is a RNA-binding residue prediction…

Predicts protein-RNA binding sites. PredRBR is a RNA-binding residue prediction method that uses the GTB algorithm for building multiple classification trees based on the 44 optimal features selected…

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circlncRNAnet
Web
Desktop

circlncRNAnet

Maps the functional networks of long or circular forms of non-coding RNAs…

Maps the functional networks of long or circular forms of non-coding RNAs (ncRNA). circlncRNAnet allows in-depth analyses of ncRNA biology. The software provides three features: (1) a framework for…

Information

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