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De novo 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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AlignACE
Desktop
Web

AlignACE Aligns Nucleic Acid Conserved Elements

A Gibbs sampling algorithm for identifying motifs that are over-represented in…

A Gibbs sampling algorithm for identifying motifs that are over-represented in a set of DNA sequences. When used to search upstream of apparently coregulated genes, AlignACE finds motifs that often…

MDscan
Desktop
Web

MDscan Motif Discovery scan

A computational method that examines the ChIP-array-selected sequences and…

A computational method that examines the ChIP-array-selected sequences and searches for DNA sequence motifs representing the protein-DNA interaction sites. MDscan combines the advantages of two…

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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

Provides peak identification in ChIP-Seq data. MICSA uses an approach combining…

Provides peak identification in ChIP-Seq data. MICSA uses an approach combining knowledge about DNA fragment coverage in ChIP and control experiments along with motif discovery. This application is…

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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 automatically…

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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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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 using…

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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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denovochipseq
Desktop

denovochipseq

A computational pipeline to extract the transcription factor binding motifs…

A computational pipeline to extract the transcription factor binding motifs from ChIP-seq data, assuming no reference genome is available. denovochipseq combines de novo assembly with statistical…

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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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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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TACO
Desktop

TACO Transcription factor Association from Complex Overrepresentation

Generalizes transcription factor (TF) dimer prediction. TACO is applicable to…

Generalizes transcription factor (TF) dimer prediction. TACO is applicable to regulatory element annotations from any source, rather than being restricted to DNase-seq datasets. It was applied to 127…

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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.

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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…

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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MFMD
Desktop

MFMD Memetic Framework for Motif Discovery

Identifies motif in DNA sequences via local search and evolution algorithms.…

Identifies motif in DNA sequences via local search and evolution algorithms. MFMD consists of a memetic algorithm that aims to resolve de novo motif discovery problem. The software constructs an…

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GSMC
Desktop

GSMC Combining Parallel Gibbs Sampling with Maximal Cliques for hunting DNA Motif

Provides an accurate method for DNA motif discovery, especially for detecting…

Provides an accurate method for DNA motif discovery, especially for detecting cofactor motifs in better large-scale ChIP-Seq data. GSMC uses Gibbs sampling to generate initial motifs and then employs…

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WSMD
Desktop

WSMD Weakly-Supervised Motif Discovery

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

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 and…

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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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