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MicroRNA target site identification software tools | CLIP-seq data analysis

MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount of miRNA-target interactions (MTIs) have…
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MicroMUMMIE
Desktop

MicroMUMMIE

A specific model, implemented within the MUMMIE framework, for predicting…

A specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.

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doRiNA
Dataset

doRiNA

Focuses in post-transcriptional regulation which integrates information related…

Focuses in post-transcriptional regulation which integrates information related to binding site data between RNA binding proteins (RBPs) and microRNAs. To enable the inclusion of doRiNA into…

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DIANA-TarBase
Dataset

DIANA-TarBase

Provides for the first time hundreds of thousands of high quality manually…

Provides for the first time hundreds of thousands of high quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. With DIANA-TarBase v7.0 you can…

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miRBShunter
Desktop

miRBShunter

Identifies canonical and non-canonical miRNA-binding sites based on de novo…

Identifies canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter extracts peak sequences,…

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MIRZA
Desktop

MIRZA

A biophysical model of miRNA-target interaction and infer its energy parameters…

A biophysical model of miRNA-target interaction and infer its energy parameters from Ago-CLIP data. MIRZA includes parameters associated with base pairs and loops and specific miRNA…

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CLIPZ
Web

CLIPZ

Allows to analyse binding sites of RNA-binding proteins. CLIPZ is a database…

Allows to analyse binding sites of RNA-binding proteins. CLIPZ is a database and an analysis environment which supports the automatic functional annotation of short reads resulting primarily from…

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starBase
Dataset

starBase

It is designed for decoding Pan-Cancer and Interaction Networks of lncRNAs,…

It is designed for decoding Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP,…

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chimiRic
Desktop

chimiRic

A model for miRNA target prediction through discriminative learning on…

A model for miRNA target prediction through discriminative learning on transcriptome-wide AGO CLIP and CLASH profiles. Our goal was to learn to accurately predict biochemical miRNA-target site…

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PARma
Desktop

PARma

A complete data analysis software for AGO-PAR-CLIP experiments to identify…

A complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites.

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miRTarCLIP
Desktop

miRTarCLIP

A systematic approach for mining miRNA-target sites from CLIP-Seq and PAR-CLIP…

A systematic approach for mining miRNA-target sites from CLIP-Seq and PAR-CLIP sequencing data, and integrated the workflow with a graphical web-based browser, which provides a user friendly…

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