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RBP binding site detection software tools | RNA modification data analysis

Motivated by the increased amount of data on protein-RNA interactions and the availability of complete genome sequences of several organisms, many computational methods have been proposed to predict binding sites in protein-RNA interactions.…
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RNAcompete
Desktop

RNAcompete

Allows the study of RNA-protein interactions. RNAcompete provides an estimate…

Allows the study of RNA-protein interactions. RNAcompete provides an estimate of relative preference for a large number of individual sequences using a single binding reaction. It also permits to…

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DeepBind
Dataset

DeepBind

An approach based on deep convolutional neural networks. DeepBind can discover…

An approach based on deep convolutional neural networks. DeepBind can discover new patterns even when the locations of patterns within sequences are unknown—a task for which traditional neural…

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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…

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…

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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…

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RBPbinding
Web

RBPbinding

Predicts protein-binding regions in mRNA. RBPbinding is a support vector…

Predicts protein-binding regions in mRNA. RBPbinding is a support vector machine (SVM) that uses sequence profiles constructed from log-odds scores of mono and di-nucleotides and nucleotide…

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RBPmap
Web

RBPmap

A web server for accurate prediction and mapping of RBP binding sites. RBPmap…

A web server for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports…

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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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SimiRa
Web

SimiRa

Compares enriched functional categories such as pathways and GO terms. SimiRa…

Compares enriched functional categories such as pathways and GO terms. SimiRa allows to find similar regulators for given input sets of microRNAs and RBPs. It was developed to act as a…

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iDeep
Desktop

iDeep

A deep learning based framework to fuse heterogeneous data for predicting…

A deep learning based framework to fuse heterogeneous data for predicting RNA-protein interaction sites. iDeep can not only learn the hidden feature patterns from individual source of data, but also…

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PTRcombiner
Desktop

PTRcombiner

A tool for the study of the combinatorial nature of post-transcriptional…

A tool for the study of the combinatorial nature of post-transcriptional trans-factors. PTRcombiner allows the identification of clusters of trans-factors (RBPs and miRNAs) from interaction maps and…

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