RBPome RBPome

An integrative resource of CLIP-seq studies

Related Tools

Lots of computational tools have been developed for analyzing CLIP-seq data and RNA-protein interaction. According to their usage, here we briefly introduce these tools and provide their website links. We hope these tools and database will be helpful for CLIP-seq and RNA-protein interaction studies.

CLIP-seq data pre-processing

FASTX-Toolkit: A short-reads pre-processing tools
PRINSEQ: Easy and rapid quality control and data preprocessing

CLIP-seq reads mapping

Bowtie: An ultrafast memory-efficient short read aligner
Novoalign: An aligner for single-ended and paired-end reads

CLIP-seq peak calling

PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data
wavClusteR: Infer RNA binding sites from PAR-CLIP data
CIMS: Crosslinking induced mutation site (CIMS) analysis
Piranha: CLIP- and RIP-Seq peak caller
CLIPper: A tool to detect CLIP-seq peaks

RIP-seq peak calling

RIPSeeker: A tool to identify protein-associated transcripts from RIP-seq experiments
ASPeak: A tool to detect peaks for RIP-Seq
Piranha: CLIP- and RIP-Seq peak caller

CLIP-seq binding preferences

MEME-ChIP: Motif-based analysis of large nucleotide data sets
Zagros: Motif discovery using CLIP-Seq data
RNAmotifs: Prediction of multivalent RNA motifs that control alternative splicing
RNAcontext: Learning the sequence and structure binding preferences of RNA-binding proteins
RNAmotif: A web server for the discovery of sequence and structure preferences of RNA-binding proteins
CapR: Revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data
GraphProt: Modeling binding preferences of RNA-binding proteins

CLIP-seq other tools

PIPE-CLIP: A comprehensive online tool for CLIP-seq data analysis
dCLIP: A computational approach for comparative CLIP-seq analyses

RBP binding site prediction

MCarts: Prediction of clustered RNA-binding protein motif sites in the mammalian genome
catRAPID: Predictor of protein-RNA interactions

CLIP-seq related database

NPInter v2.0: An updated database of ncRNA interactions
AURA 2: The atlas of UTR regulatory activity
starBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
doRiNA: A database of RNA interactions in post-transcriptional regulation
CLIPZ: A database and analysis environment for experimentally determined binding sites of RNA-binding proteins

RNA-binding protein database

RBPDB: The database of RNA-binding specificities
CISBP-RNA: The online library of RNA binding proteins and their motifs
RNAcompete: Web supplement to "A compendium of RNA-binding motifs for decoding gene regulation"