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Motif discovery software tools | CLIP-seq data analysis

High-throughput protein-RNA interaction data generated by CLIP-seq has provided an unprecedented depth of access to the activities of RNA-binding proteins (RBPs), the key players in co- and post-transcriptional regulation of gene expression. Motif…
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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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pyCRAC
Desktop

pyCRAC

Permits the analysis of Nrd1-Nab3-RNA interactions. pyCRAC combines many…

Permits the analysis of Nrd1-Nab3-RNA interactions. pyCRAC combines many popular cross-linking and immunoprecipitation (CLIP)/ cross-linking and cDNA analysis (CRAC) analysis methods. It can be used…

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RNAmotifs
Desktop

RNAmotifs

Recognizes clusters of motifs underlying regulatory principles of alternative…

Recognizes clusters of motifs underlying regulatory principles of alternative splicing and alternative polyadenylation. RNAmotifs computes an enrichment score (ES) on the super-imposed sequences of…

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GraphProt
Desktop

GraphProt

It can be used for modeling binding preferences of RNA-binding proteins from…

It can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

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mCarts
Desktop

mCarts

A hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

A hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

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RBPmotif
Web

RBPmotif

Implements tools to identify binding preferences of RNA-binding proteins (RBPs).

Implements tools to identify binding preferences of RNA-binding proteins (RBPs).

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BEAM
Desktop

BEAM BEAr Motif finder

A method for structural motif discovery from a set of unaligned RNAs. BEAM…

A method for structural motif discovery from a set of unaligned RNAs. BEAM explores sets of unaligned RNAs sharing a biological property, looking for the most represented local secondary structure…

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deepnet-rbp
Desktop

deepnet-rbp

A deep learning framework to model the binding preferences of RNA-binding…

A deep learning framework to model the binding preferences of RNA-binding proteins (RBPs) by integrating the primary sequence, predicted secondary and tertiary structural profiles of the target…

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RNApeakFold
Desktop

RNApeakFold

Calculates the probable RNA secondary structure through computational folding.…

Calculates the probable RNA secondary structure through computational folding. RNApeakFold is an RNA secondary structure prediction tool tailored to CLIP peaks. It first computes base pairing…

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RNAcontext
Desktop
Web

RNAcontext

A motif finding method ideally suited for using large-scale RNA-binding…

A motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures.

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Zagros
Desktop

Zagros

A motif discovery software for CLIP-Seq high-throughput protein-RNA interaction…

A motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data. Given the regions of significant enrichment for reads Zagros can characterize the binding site for the given RBP.…

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CapR
Desktop

CapR

Calculates the probability that each RNA base position is located within each…

Calculates the probability that each RNA base position is located within each secondary structural context. Six contexts of RNA secondary structures were taken into account, according to the…

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ssHMM
Desktop

ssHMM Sequence-structure hidden Markov model

Identifies de novo sequence-structure motifs in a set of RNA sequences bound by…

Identifies de novo sequence-structure motifs in a set of RNA sequences bound by a certain RNA-binding proteins (RBP). ssHMM combines a hidden Markov model (HMM) with Gibbs sampling to learn the joint…

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MEMERIS
Desktop

MEMERIS Multiple Em for Motif Elucidation in Rna’s Including secondary Structures

A computational method for searching sequence motifs in a set of RNA sequences…

A computational method for searching sequence motifs in a set of RNA sequences and simultaneously integrating information about secondary structures. MEMERIS precomputes values that characterize the…

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ProfileSeq
Desktop

ProfileSeq

Performs a quantitative comparison between profiles of genome-based signal.…

Performs a quantitative comparison between profiles of genome-based signal. ProfileSeq allows for straightforward determination and correction of confounding factors. It permits to take into account…

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DeMo
Desktop

DeMo Deep Motif

Provides a convolutional/highway multilayer perceptron (MLP) network. DeMo DeMo…

Provides a convolutional/highway multilayer perceptron (MLP) network. DeMo DeMo is a generic model for visualizing sequence classification tasks. It outperforms the state-of-the-art baseline for 92…

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RCK
Desktop

RCK RNAcontext k-mer

Infers protein-RNA preferences from RNAcompete experimental data. RCK is a…

Infers protein-RNA preferences from RNAcompete experimental data. RCK is a software which uses a k-mer based model for sequence preferences and specific structural context preferences for each k-mer…

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DeBooster
Desktop

DeBooster Deep Boost

A framework to predict the sequence specificities of RNA-binding proteins from…

A framework to predict the sequence specificities of RNA-binding proteins from high-throughput CLIP-seq data. DeBooster provides an effective index to identify pathogenic mutations from normal…

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MatrixREDUCE
Desktop

MatrixREDUCE

Discovers the position-specific affinity matrices for unknown RNAbinding…

Discovers the position-specific affinity matrices for unknown RNAbinding factors and infers their condition-specific activities. MatrixREDUCE uses genome-wide occupancy data for a transcription…

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