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CLIP-seq data analysis bioinformatics software tools

Cross-Linking Immunoprecipitation associated to high-throughput sequencing (CLIP-seq) is a technique used to identify RNA directly bound to RNA-binding proteins across the entire transcriptome in cell or tissue samples. Recent technological and computational advances permit the…

CLIP-seq analysis steps

Experts in CLIP-seq analysis

They share and annotate bioinformatics tools

Most recent bioinformatics tools

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circTools
Web

circTools

Allows the discovery of circRNAs and their interactions with miRNAs. circTools…

Allows the discovery of circRNAs and their interactions with miRNAs. circTools investigates the high-throughput AGO CLIP-Seq and RNA-Seq data to proceed. It employs functionalities of circSeeker,…

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clipSearch
Desktop

clipSearch

Finds interactions between circRNAs and miRNAs from CLIP-Seq datasets.…

Finds interactions between circRNAs and miRNAs from CLIP-Seq datasets. clipSearch identifies the seed that matches in AGO-binding sites to proceed.

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circAnno
Desktop

circAnno

Allows annotation of exon boundaries and circRNAs. circAnno provides the exons…

Allows annotation of exon boundaries and circRNAs. circAnno provides the exons from known gene annotation.

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circScan
Desktop

circScan

Recognizes back-splicing junctions of circular RNAs (circRNAs) from…

Recognizes back-splicing junctions of circular RNAs (circRNAs) from crosslinking and immunoprecipitation (CLIP-seq) datasets. circScan creates full read alignments with back-splicing signals. It can…

Most popular analytical software and databases

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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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MiClip
Desktop

MiClip

A model-based approach to identify high-confidence protein-RNA binding sites…

A model-based approach to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize…

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