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Enhancer detection software tools | Genome annotation

Enhancers are of short regulatory DNA elements. They can be bound with proteins (activators) to activate transcription of a gene, and hence play a critical role in promoting gene transcription in eukaryotes. With the avalanche of DNA sequences…
G T A T C G C T A
ChromHMM
Desktop

ChromHMM

A software program for learning and characterizing chromatin states. ChromHMM…

A software program for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the…

gkmSVM
Desktop

gkmSVM gapped-kmer-SVM

Detects functional sequence elements in regulatory DNA. gkmSVM is trained to…

Detects functional sequence elements in regulatory DNA. gkmSVM is trained to detect regulatory DNA elements active in a cell type by using chromatin accessible DNA sequences as the positive set and a…

G T A T C G C T A
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…

VISTA Enhancer…
Dataset

VISTA Enhancer Browser

A central resource for experimentally validated human and mouse noncoding…

A central resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. The purpose of VISTA Enhancer Browser is to facilitate…

G T A T C G C T A
Segway
Desktop

Segway

Contains a method for analyzing multiple tracks of functional genomics data.…

Contains a method for analyzing multiple tracks of functional genomics data. Segway uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even…

LS-GKM
Desktop

LS-GKM

Allows users to apply gapped-kmer-SVM (gkmSVM) approach on large scale…

Allows users to apply gapped-kmer-SVM (gkmSVM) approach on large scale datasets. LS-GKM implements gapped k-mer kernel (gkm-kernel) functions within the LIBSVM framework. The software aims to improve…

EMERGE
Desktop

EMERGE

A flexible and user-friendly tool to integrate the information from different…

A flexible and user-friendly tool to integrate the information from different types of genomic datasets, e.g. ATAC-seq, ChIP-seq, conservation, aiming to increase the ease and success rate of…

i-cisTarget
Web

i-cisTarget

An integrative genomics method for the prediction of regulatory features and…

An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly. ii-cisTarget enables: (i) to detect transcription factor motifs in a set…

BiRen
Desktop

BiRen

Predicts enhancers using the DNA sequence alone. BiRen can learn common…

Predicts enhancers using the DNA sequence alone. BiRen can learn common enhancer patterns directly from the DNA sequence and exhibits superior accuracy, robustness, and generalizability in enhancer…

DEEP
Desktop

DEEP

An ensemble prediction framework. DEEP integrates three components with diverse…

An ensemble prediction framework. DEEP integrates three components with diverse characteristics that streamline the analysis of enhancer's properties in a great variety of cellular conditions.…

PETModule
Desktop

PETModule Predicting enhancer target by modules

A motif module based approach that predicts ETG pairs through a motif module…

A motif module based approach that predicts ETG pairs through a motif module based approach. PETModule integrates the conservation, distance, enhancer-promoter activity correlation used previously…

EnhancerAtlas
Dataset

EnhancerAtlas

An interactive database which contains an atlas of 2,534,123 enhancers for 105…

An interactive database which contains an atlas of 2,534,123 enhancers for 105 cell/tissue types. A consensus enhancer annotation was obtained for each cell by summation of independent experimental…

iEnhancer-2L
Web

iEnhancer-2L

Identifies enhancers and their strength by pseudo k-tuple nucleotide…

Identifies enhancers and their strength by pseudo k-tuple nucleotide composition. iEnhancer-2L is a two-layer predictor. Its 1st layer is to identify whether a query DNA element is of enhancer or…

LMethyR-SVM
Algorithm

LMethyR-SVM

A framework for the prediction of enhancers using cell-type-specific…

A framework for the prediction of enhancers using cell-type-specific low-methylated regions (LMRs) detected from the whole genome bisulfite sequencing (WGBS) data. In LMethyR-SVM, the set of…

LEG
Web

LEG Limb-Enhancer Genie

Predicts enhancers active in developing limbs. LEG is a web interface that…

Predicts enhancers active in developing limbs. LEG is a web interface that provides two analysis modes: (1) one mod that finds the overlap of a set of input regions using predicted limb enhancers and…

A catalogue of…
Dataset

A catalogue of functional enhancers in hESCs

Provides the means to refine models of the regulatory circuitry. The catalogue…

Provides the means to refine models of the regulatory circuitry. The catalogue of functional enhancers in human Embryonic Stem Cells (hESCs) is a database that encompasses a comprehensive collection…

NaviSE
Desktop

NaviSE

Processes and integrates multiple genome-wide Next Generation Sequencing (NGS)…

Processes and integrates multiple genome-wide Next Generation Sequencing (NGS) epigenomics signals from various input file formats into an interactive HTML report. NaviSE was designed to perform…

EP-sim
Desktop

EP-sim

An alignment-free statistic for the classification of cis-regulatory modules,…

An alignment-free statistic for the classification of cis-regulatory modules, called 2EP2∗, that is based on multiple resolution patterns derived from the Entropic Profiles (EPs). The Entropic…

Database of EI…
Dataset

Database of EI candidate tissue-specific enhancers

A database of candidate tissue-specific enhancers in human and mouse. The…

A database of candidate tissue-specific enhancers in human and mouse. The database of EI candidate tissue-specific enhancers provides further support for the notion that sequence-based features in…

p300enhancer
Desktop

p300enhancer

A discriminative computational framework to detect enhancers from DNA sequence…

A discriminative computational framework to detect enhancers from DNA sequence alone that does not rely on conservation or known transcription factor binding specificities. We use a support vector…

DELTA
Desktop

DELTA Distal Enhancer Locating Tool based on AdaBoost

A framework for accurately identifying enhancers from epigenetic data across…

A framework for accurately identifying enhancers from epigenetic data across multiple cell types. We show that DELTA significantly outperforms current enhancer prediction methods in prediction…

EnhancerPred
Web

EnhancerPred

Formulates the prediction of enhancers and their strength as a binary…

Formulates the prediction of enhancers and their strength as a binary classification problem and solves it using a machine learning algorithm. EnhancerPred extracts features using BPB, NC and PseNc…

PEDLA
Desktop

PEDLA

A deep learning-based algorithmic framework to systematically and precisely…

A deep learning-based algorithmic framework to systematically and precisely predict enhancers on a genome-wide scale using heterogeneous types of data. PEDLA has three outstanding characteristics…

EnhancerFinder
Desktop

EnhancerFinder

Allows the seamless integration of feature data from a variety of experimental…

Allows the seamless integration of feature data from a variety of experimental techniques and biological contexts that have previously been used individually to predict enhancers. One motivation for…

CLARE
Web

CLARE Cracking the LAnguage of Regulatory Elements

A computational method designed to reveal sequence encryption of…

A computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it…

CSI-ANN
Desktop

CSI-ANN

A computational framework for identifying functional DNA elements using…

A computational framework for identifying functional DNA elements using chromatin signatures. The framework consists of a data transformation and a feature extraction step followed by a…

RFECS
Desktop

RFECS Random Forest based Enhancer identification from Chromatin States

A Random-Forest based algorithm to integrate histone modification profiles for…

A Random-Forest based algorithm to integrate histone modification profiles for identification of enhancers, and used it to identify enhancers in a number of cell-types. RFECS not only leads to more…

IM-PET
Web
Desktop

IM-PET Integrated Methods for Predicting Enhancer Targets

An integrated method for predicting enhancer targets. Leveraging abundant omics…

An integrated method for predicting enhancer targets. Leveraging abundant omics data, we develop multiple features and integrate them probabilistically to make robust predictions of…

zTrap
Dataset

zTrap

A useful resource to find gene trap and enhancer trap fish lines that express…

A useful resource to find gene trap and enhancer trap fish lines that express GFP and Gal4FF in desired patterns, and to find insertions of the gene trap and enhancer trap constructs that are located…

ROSE
Desktop

ROSE Rank Ordering of Super-Enhancers

Permits to differentiate super-enhancers from typical enhancers. ROSE uses…

Permits to differentiate super-enhancers from typical enhancers. ROSE uses sequencing data to proceed. It takes as input a file of previously identified constituent enhancers.

ChromaGenSVM
Desktop

ChromaGenSVM

A method for chromatin state detection using support vector machines in…

A method for chromatin state detection using support vector machines in combination with genetic algorithm optimization. ChromaGenSVM selects optimum combinations of specific histone epigenetic marks…

DENdb
Dataset

DENdb Dragon Enhancers database

A centralized on-line repository of predicted enhancers derived from multiple…

A centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods (ChromHMM, Segway, RFECS, CSI-ANN, and…

ZETRAP
Dataset

ZETRAP Zebrafish Enhancer TRAP transgenic line database

A web-based system that provides data and information to the scientific…

A web-based system that provides data and information to the scientific community about the developmental, genetic and genomic aspects of transgenic zebrafish lines obtained using Tol2…

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