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Motif discovery software tools | ChIP sequencing data analysis

De novo motif discovery is a difficult computational task. Historically, dedicated algorithms always reported a high percentage of false positives. Their performance did not improve considerably even after they adapted to handle large amounts of…
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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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MEME Suite
Web

MEME Suite

Provides a unified portal for online discovery and analysis of sequence motifs…

Provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery…

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kmerHMM
Desktop

kmerHMM

Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov…

Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and Belief Propagation.

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Weeder
Desktop
Web

Weeder

Falls into the motif enumeration family of motif discovery tools in which the…

Falls into the motif enumeration family of motif discovery tools in which the occurrence of motifs in the query sequences are counted and, in this case, compared to a pre-calculated set of genome…

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EXTREME
Desktop

EXTREME

A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and…

A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data.

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RSAT peak-motifs
Web

RSAT peak-motifs Regulatory Sequence Analysis Tools peak-motifs

A computational pipeline that discovers motifs in peak sequences, compares them…

A computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genome browser and generates an extensive…

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DRIMust
Web

DRIMust Discovering Rank Imbalanced Motifs using suffix trees

Searches for enrichment of motifs in large datasets of DNA, RNA or protein…

Searches for enrichment of motifs in large datasets of DNA, RNA or protein sequences. DRIMust is a web application whose algorithm is based on the minimum hypergeometric statistical framework and…

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kmer-SVM
Web

kmer-SVM

A tool suite designed to aid in analysis of next-generation sequencing (NGS)…

A tool suite designed to aid in analysis of next-generation sequencing (NGS) data. kmer-SVM uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of…

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DMINDA
Web

DMINDA DNA Motif Identification aND Analyses

Allows to indentify and analyse regulatory DNA motif. DMINDA is a motif…

Allows to indentify and analyse regulatory DNA motif. DMINDA is a motif analysis web server that contains six motif analysis functions: i) motif finding; (ii) motif scanning; (iii) motif comparison;…

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LASAGNA-Search
Web

LASAGNA-Search

A user-friendly and an easy-to-use webtool for transcription factor binding…

A user-friendly and an easy-to-use webtool for transcription factor binding site (TFBS) search and visualization. LASAGNA-Search offers collections of 1792 TF models built from either TFBSs or…

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SCOPE
Web

SCOPE Suite for Computational identification Of Promoter Elements

An ensemble of programs aimed at identifying novel cis-regulatory elements from…

An ensemble of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE motif finder uses an ensemble of three programs behind the scenes to identify…

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BETA
Desktop

BETA Binding and Expression Target Analysis

A software package that integrates ChIP-seq of transcription factors or…

A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.

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motifRG
Desktop

motifRG

A package based on an algorithm for discovering differential motifs between two…

A package based on an algorithm for discovering differential motifs between two sequence datasets that is effective in eliminating systematic biases and scalable to large datasets. motifRG measures…

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PRISM
Desktop

PRISM

Offers a comprehensive genomic approach to transcription factor function…

Offers a comprehensive genomic approach to transcription factor function prediction.

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MICSA
Desktop

MICSA Motif Identification for ChIP-Seq Analysis

A package for the identification of transcription factor binding sites in…

A package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie…

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LedPred
Desktop

LedPred

A flexible support vector machines (SVM) workflow that predicts new regulatory…

A flexible support vector machines (SVM) workflow that predicts new regulatory sequences based on the annotation of known cis-regulatory modules (CRMs), which are associated to a large variety of…

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Arpeggio
Desktop

Arpeggio

Harmonic compression of ChIP-seq data reveals protein-chromatin interaction…

Harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

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SIOMICS
Desktop

SIOMICS Systematic Identification Of Motifs In ChIP-Seq data

A software developed to de novo identify motifs in large sequence datasets such…

A software developed to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.

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PscanChIP
Web

PscanChIP

A web server that, starting from a collection of genomic regions derived from a…

A web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices,…

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rGADEM
Desktop

rGADEM

A package containing an extended version of the original GADEM C code. For…

A package containing an extended version of the original GADEM C code. For ChIP-Seq data, a key improvement is that, on multicore computers, rGADEM can take advantage of multithreading via Grand…

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ChIPMunk
Desktop

ChIPMunk

A fast heuristic DNA motif digger based a on greedy approach accompanied by…

A fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping.

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BaMM!motif
Desktop

BaMM!motif Bayesian Markov Model motif discovery

A Bayesian approach for motif discovery using Markov models in which…

A Bayesian approach for motif discovery using Markov models in which conditional probabilities of order k−1 act as priors for those of order k. This Bayesian Markov model (BMM) training…

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Discrover
Desktop

Discrover DISCRiminative and discOVER

Discovers sequence motifs of protein binding-site patterns in nucleic acid…

Discovers sequence motifs of protein binding-site patterns in nucleic acid sequences. Discrover is based on a discriminative learning method and on a Hidden Markov Model (HMM). It allows user to…

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GEM
Desktop

GEM Genome wide Event finding and Motif discovery

Resolves the location of protein-DNA interactions and discovers explanatory DNA…

Resolves the location of protein-DNA interactions and discovers explanatory DNA sequence motifs. GEM integrates model of ChIP-Seq or ChIP-exo reads and proximal DNA sequences. It makes binding…

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TherMos
Desktop

TherMos THERmodynamic MOdeling of ChIP-Seq

Estimates protein–DNA binding energies from in vivo binding profiles. TherMos…

Estimates protein–DNA binding energies from in vivo binding profiles. TherMos is a position specific energy matrix (PSEM) estimation method. The software infers an additive binding energy model…

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MotifHyades
Desktop

MotifHyades

Provides a probabilistic model for de novo DNA motif pair discovery on paired…

Provides a probabilistic model for de novo DNA motif pair discovery on paired sequences. MotifHyades is more accurate than the previous ad hoc computational pipeline for DNA motif pair discovery. In…

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IMMBoost
Desktop

IMMBoost

Predicts cis-regulatory modules (CRMs) active in a specific expression domain.…

Predicts cis-regulatory modules (CRMs) active in a specific expression domain. IMMBoost is a supervised learning method and a two-stage learning method: the first stage uses the previously…

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PAD
Web
Desktop

PAD Proximal And Distal

Identify chromatin immunoprecipitation of 104 DNA binding proteins in embryonic…

Identify chromatin immunoprecipitation of 104 DNA binding proteins in embryonic stem cell (ESC) lines co-localization at these respective regions. PAD was applied to characterize protein…

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KeBABS
Desktop

KeBABS Kernel-Based Analysis of Biological Sequences

Provides functionality for kernel based analysis of biological sequences via…

Provides functionality for kernel based analysis of biological sequences via support vector machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence…

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USeq
Desktop

USeq

A collection of software tools for for both low and high level analysis of next…

A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.

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GimmeMotifs
Desktop

GimmeMotifs

A pipeline that incorporates an ensemble of computational tools to predict…

A pipeline that incorporates an ensemble of computational tools to predict motifs de novo from ChIP-sequencing (ChIP-seq) data. Similar redundant motifs are compared using the weighted information…

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TFFM
Desktop

TFFM

The Transcription Factor Flexible Models (TFFMs) represent TFBSs and are based…

The Transcription Factor Flexible Models (TFFMs) represent TFBSs and are based on hidden Markov models (HMM). They are flexible and are able to model both position interdependence within TFBSs and…

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CompleteMOTIFs
Web

CompleteMOTIFs

A motif discovery platform developed to help biologists to find novel as well…

A motif discovery platform developed to help biologists to find novel as well as known motifs in their peak datasets from transcription factor (TF) binding experiments such as ChIP-seq and ChIP-chip.…

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MoTeX-II
Desktop

MoTeX-II

Allows to structure motif extraction from large-scale datasets. MoTeX-II is a…

Allows to structure motif extraction from large-scale datasets. MoTeX-II is a word-based high performance computing (HPC) tool which uses state-of-the-art algorithms for solving the fixed-length…

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diChIPMunk
Desktop

diChIPMunk

A computational tool that constructs transcription factor binding sites TFBS…

A computational tool that constructs transcription factor binding sites TFBS models as optimal dinucleotide PWMs, thus accounting for correlations between nucleotides neighboring in input sequence.…

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DiMO
Desktop

DiMO Discriminative Motif Optimizer

Takes a seed motif along with a positive and a negative database and improves…

Takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy.

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MEME-ChIP
Web

MEME-ChIP

A web-based tool for analyzing motifs in large DNA or RNA data sets. MEME-ChIP…

A web-based tool for analyzing motifs in large DNA or RNA data sets. MEME-ChIP can analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and related assays, as well…

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oPOSSUM
Web

oPOSSUM

A web-based system for the detection of over-represented conserved…

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

CentriMo
Desktop
Web

CentriMo

Identifies known or user-provided motifs that show a significant preference for…

Identifies known or user-provided motifs that show a significant preference for particular locations in your nucleotide sequences. CentriMo can also show if the local enrichment is significant…

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WSMD
Desktop

WSMD Weakly-Supervised Motif Discovery

Identifies motifs from ChIP-seq datasets. WSMD allows “global” optimization…

Identifies motifs from ChIP-seq datasets. WSMD allows “global” optimization of position weight matrices (PWMs) in continuous space, thereby reducing the information loss of model representation…

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Repliscan
Desktop

Repliscan

Detects and classifies regions of replication across the genome. Repliscan…

Detects and classifies regions of replication across the genome. Repliscan normalizes automatically, removes outlying and uninformative data points, and classifies Repli-seq signals into discrete…

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THiCweed
Desktop

THiCweed

Offers both speed and accuracy in finding multiple motifs in large datasets.…

Offers both speed and accuracy in finding multiple motifs in large datasets. THiCweed achieves its combination of speed and accuracy without resorting to heuristics in scoring and without resorting…

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RCADE
Desktop
Web

RCADE Recognition Code-Assisted Discovery of regulatory Elements

A software tool for motif discovery from Cys2His2 zinc finger (C2H2-ZF)…

A software tool for motif discovery from Cys2His2 zinc finger (C2H2-ZF) ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that…

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RPMCMC
Desktop

RPMCMC Repulsive Parallel Markov Chain Monte Carlo

A parallel version of the widely used Gibbs motif sampler. RPMCMC is run on…

A parallel version of the widely used Gibbs motif sampler. RPMCMC is run on parallel interacting motif samplers. A repulsive force is generated when different motifs produced by different samplers…

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coMOTIF
Desktop

coMOTIF

Considers two motifs jointly and simultaneously determines which sequences…

Considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. coMOTIF can take a single position weight matrice (PWM) and…

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MotifLab
Desktop

MotifLab

A general workbench for analysing regulatory sequence regions and discovering…

A general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab can improve performance of binding site…

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PairMotifChIP
Desktop

PairMotifChIP

Processes large DNA data sets. PairMotifChIP is an efficient method for…

Processes large DNA data sets. PairMotifChIP is an efficient method for extracting pairs of I-mers. It obtains motifs by combining extracted I-mers based on clustering methods. The tool is able to…

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SeqGL
Desktop

SeqGL

Identifies multiple TF sequence signals from ChIP-, DNase-, and ATAC-seq…

Identifies multiple TF sequence signals from ChIP-, DNase-, and ATAC-seq profiles. SeqGL trains a discriminative model using a k-mer feature representation together with group lasso regularization to…

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COPS
Desktop

COPS

Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding…

Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.

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MOCCS
Desktop

MOCCS MOtif Centrality analysis of ChIP-Seq

Clarifies the DNA-binding motif ambiguity using ChIP-seq data. Given the…

Clarifies the DNA-binding motif ambiguity using ChIP-seq data. Given the protocol of ChIP experiments and data size of high-throughput sequencing, the frequency distribution of any sequence pattern…

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CTF
Desktop

CTF Crf-based Tfbs Finding system

Predicts transcription factor binding sties (TFBSs). CTF is based on…

Predicts transcription factor binding sties (TFBSs). CTF is based on Conditional Random Fields (CRFs) and can capture sophisticated dependency and integrate information from different sources. The…

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HMS
Desktop

HMS Hybrid Motif Sampler

Implements a computational algorithm specifically designed for transcription…

Implements a computational algorithm specifically designed for transcription factor binding sites (TFBS) motif discovery using ChIP-Seq data. HMS combines stochastic sampling with deterministic…

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EXRANGES
Desktop

EXRANGES Expression in a Rate-Normalized GEne Specific

Adjusts how expression data is provided to the network algorithm. ExRANGES…

Adjusts how expression data is provided to the network algorithm. ExRANGES prioritizes targets differently than traditional expression and improves the ability of these networks to accurately predict…

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PMMdeNovo
Desktop

PMMdeNovo

A stochastic algorithm for performing robust model selection in a latent…

A stochastic algorithm for performing robust model selection in a latent variable setting. This algorithm yields a solution without relying on hyperparameter-tuning via massive cross-validation or…

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SeqSite
Desktop

SeqSite ChIP-Seq Binding Site Identification

It was developed for detecting transcription factor binding sites from ChIP-seq…

It was developed for detecting transcription factor binding sites from ChIP-seq data.

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ChIPModule
Desktop

ChIPModule

Systematic discovery of transcription factors and their cofactors from ChIP-seq…

Systematic discovery of transcription factors and their cofactors from ChIP-seq data.

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ChIPseek
Web

ChIPseek

A web-based tool for ChIP data analysis providing summary statistics in graphs…

A web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses.

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STEME
Desktop
Web

STEME Suffix Tree EM for Motif Elicitation

An approximation to the Expectation-Maximisation algorithm for the type of…

An approximation to the Expectation-Maximisation algorithm for the type of model used in motif finders such as MEME. STEME’s EM approximation runs an order of magnitude more quickly than the MEME…

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Factorbook…
Web

Factorbook Motif Pipeline

Performs de novo motif search, subsequent filtering and discovering similar…

Performs de novo motif search, subsequent filtering and discovering similar motifs in the databases from genomic regions defined by user in NarrowPeak or BED formats sorted by peak strengths.…

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SVM2CRM
Desktop

SVM2CRM

Detects cis-regulatory elements using svm implemented in LiblineaR. This…

Detects cis-regulatory elements using svm implemented in LiblineaR. This function require as input a bed file in format chr, start, end, signalNorm. The genomic coordinates must be sort. The data…

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Consensus
Desktop
Web

Consensus

Determines consensus patterns in unaligned sequences. Consensus is based on a…

Determines consensus patterns in unaligned sequences. Consensus is based on a matrix representation of a consensus pattern.

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W-ChIPMotifs
Web

W-ChIPMotifs

A web application tool that provides a user friendly interface for de novo…

A web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed…

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DREME
Desktop
Web

DREME

A motif discovery algorithm specifically designed to find the short, core…

A motif discovery algorithm specifically designed to find the short, core DNA-binding motifs of eukaryotic TFs, and optimized to analyze very large ChIP-seq datasets in minutes. DREME is available as…

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LocalMotif
Desktop

LocalMotif

A software tool for discovering transcription factor binding motifs in a…

A software tool for discovering transcription factor binding motifs in a collection of DNA sequences. The uniqueness of LocalMotif lies in its ability to discover motifs that occur localized in…

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CisFinder
Desktop
Web

CisFinder

A tool for finding over-representing short DNA motifs (e.g., transcription…

A tool for finding over-representing short DNA motifs (e.g., transcription factor binding motifs) and estimates the Position Frequency Matrix (PFM) directly from word counts. It is designed for the…

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Promzea
Web

Promzea

A Perl-based application to discover de novo motifs underlying co-regulated…

A Perl-based application to discover de novo motifs underlying co-regulated genes in maize, Arabidopsis or rice. Promzea was validated in silico by its ability to retrieve benchmark motifs and…

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LONUT
Desktop

LONUT LOcating Non-Unique matched Tags

IImproves detection of the enriched regions for both ChIP-seq and MBD-seq data.…

IImproves detection of the enriched regions for both ChIP-seq and MBD-seq data. LONUT is an algorithm that applies a linear and polynomial regression model to establish an empirical score (ES)…

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MotifCatcher
Desktop

MotifCatcher

An integrated framework for motif discovery. MotifCatcher extends the…

An integrated framework for motif discovery. MotifCatcher extends the sensitivity of existing motif-finding tools by employing random sampling to effectively remove non-motif-containing sequences…

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SEME
Desktop

SEME Sampling with Expectation maximization for Motif Elicitation

A motif finding algorithm. SEME assumes the set of input sequences is a mixture…

A motif finding algorithm. SEME assumes the set of input sequences is a mixture of two models: a motif model and a background model. It uses unsupervised mixture model learning to learn the motif…

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GALF-P
Desktop

GALF-P Genetic Algorithm with Local Filtering and Post-processing

A framework for TFBS identification (motif discovery) in DNA sequences. It…

A framework for TFBS identification (motif discovery) in DNA sequences. It consists of Genetic Algorithm with Local Filtering (GALF) and the post-processing procedure based on adaptive adding and…

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MET
Web

MET Motif Enrichment Tool

Takes user-defined gene sets and identifies significantly associated sets of…

Takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif.

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TFBSGroup
Desktop

TFBSGroup

Identifies motifs under the ZOMOP constraint. TFBSGroup is an algorithm that…

Identifies motifs under the ZOMOP constraint. TFBSGroup is an algorithm that extracts dense subgraphs from an N-partite graph using a fast community detection algorithm designed for processing…

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FMotif
Desktop

FMotif Fast Motif

A heuristic method to extract motifs from sequences. FMotif is an algorithm…

A heuristic method to extract motifs from sequences. FMotif is an algorithm able to find motif in synthetic samples without being given the length of a predicted motif. It can identify these motifs…

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LocaMo Finder
Web

LocaMo Finder Local Motif Finder

Detects regulatory motifs based on their local over-representation in sets of…

Detects regulatory motifs based on their local over-representation in sets of regulatory regions. LocaMo Finder is based on a non-parametric approach for sample density estimation, with adjustments…

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