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Cis-regulatory module detection software tools | Genome annotation

Differential gene expression is the fundamental mechanism underlying animal development and cell differentiation. However, it is a challenge to identify comprehensively and accurately the DNA sequences that are required to regulate gene expression:…
BoBro
Desktop

BoBro

Provides a useful tool for motif identification and analysis complementary to…

Provides a useful tool for motif identification and analysis complementary to the existing tools. BoBro is a method that (i) can reliably identify statistically significant cis-regulatory motifs at a…

Promoter-Expres…
Web

Promoter-Express

Allows users to find condition-specific for transcription factor binding sites…

Allows users to find condition-specific for transcription factor binding sites (TFBSs). Promoter-Express identifies cis-regulatory elements on the DNA. It is able to retrieve a nucleotide sequence…

jPREdictor
Desktop

jPREdictor

Provides versatile prediction of cis-regulatory elements. jPREdictor allows for…

Provides versatile prediction of cis-regulatory elements. jPREdictor allows for flexible definitions of any kind of cis-regulatory element by combining individual motifs, such as transcription factor…

Imogene
Web
Desktop

Imogene

A set of statistical tools and a computer software able to predict de novo…

A set of statistical tools and a computer software able to predict de novo relevant motifs in a set of functionally related of cis-regulatory modules (CRMs) and able to infer novel CRMs. Imogene…

MCAST
Desktop
Web

MCAST Motif Cluster Alignment and Search Tool

Uses a motif-based hidden Markov model to scan for clusters of motifs. Its key…

Uses a motif-based hidden Markov model to scan for clusters of motifs. Its key features include a scoring scheme based on p-values and a method for calibrating the resulting scores to obtain…

INSECT
Web

INSECT IN-silico SEarch for Co-occurring Transcription factors

Allows to analyze genomic sequence data for in silico cis-regulatory modules…

Allows to analyze genomic sequence data for in silico cis-regulatory modules (CRMs) prediction and analysis. INSECT is a web server which allows a complete and flexible analysis of the predicted…

GibbsModule
Desktop

GibbsModule

An algorithm for de novo detection of cis-regulatory motifs (CRMs) and modules…

An algorithm for de novo detection of cis-regulatory motifs (CRMs) and modules in eukaryote genomes. GibbsModule identifies the locations of a core motif that is shared by a set of CRMs. It can…

ModuleMaster
Desktop

ModuleMaster

Finds cis-regulatory modules (CRMs) in sets of co-expressed genes. ModuleMaster…

Finds cis-regulatory modules (CRMs) in sets of co-expressed genes. ModuleMaster is a sophisticated program for large-scale batch processing. This algorithm provides a workbench for automated and…

SMCis
Algorithm

SMCis

A probabilistic modeling method for predicting cis-regulatory modules (CRMs)…

A probabilistic modeling method for predicting cis-regulatory modules (CRMs) that builds a more powerful CRM discovery model based on an HSMM (hidden semi-Markov model). SMCis characterizes the…

Haystack
Desktop

Haystack

Allows characterization of hotspots of epigenetic variability across different…

Allows characterization of hotspots of epigenetic variability across different cell-types. Haystack can be applied to epigenetic mark and supplies a method to study cell-type identity and the…

Cister
Web
Desktop

Cister Cis-element Cluster Finder

A hidden Markov model based method for detecting regulatory regions in DNA…

A hidden Markov model based method for detecting regulatory regions in DNA sequences, by searching for clusters of cis-elements. Cister is available through a website with a straightforward form to…

MONKEY
Desktop

MONKEY

Identifies conserved transcription factor binding sites (TFBSs) in sequence…

Identifies conserved transcription factor binding sites (TFBSs) in sequence alignments from multiple related species. MONKEY extends probabilistic models of binding specificity to multiple species…

MoAn
Desktop

MoAn Motif Annealer

Identifies transcription factor binding sites (TFBS) in promoters using a…

Identifies transcription factor binding sites (TFBS) in promoters using a discriminatory approach with a large negative set encompassing a significant sample of the promoters from the relevant…

MSCAN
Web

MSCAN

A leading method for binding site cluster detection that determines the…

A leading method for binding site cluster detection that determines the significance of observed sites while correcting for local compositional bias of sequences. MSCAN is highly flexible, applying…

MycoRRdb
Dataset

MycoRRdb Mycobacterium Regulatory Region Database

Aims to identify the putative cis- regulatory sequences. MycoRRdb is a database…

Aims to identify the putative cis- regulatory sequences. MycoRRdb is a database that contains list of Reciprocal Best BLAST Hits (RBBHs) for more than 20 mycobacterial species. A search mode is…

NHR-scan
Web

NHR-scan

A flexible Hidden Markov Model (HMM) framework capable of predicting nuclear…

A flexible Hidden Markov Model (HMM) framework capable of predicting nuclear hormone receptor (NHR) binding sites in genomic sequences. NHR-scan supports Viterbi and Forward algorithm scoring,…

CORECLUST
Desktop

CORECLUST COnservative REgulatory CLUster STructure

Predicts cis-regulatory modules (CRMs) based on known positional weight…

Predicts cis-regulatory modules (CRMs) based on known positional weight matrices (PWMs). CORECLUST uses an HMM-based technique to predict CRMs given known motifs for a set of system-specific…

RISO-Dynamic
Desktop

RISO-Dynamic

Allows users to identify cis-regulatory modules (CRM) in genomic sequences.…

Allows users to identify cis-regulatory modules (CRM) in genomic sequences. RISO-Dynamic provides several information about motif discovered as a header with a summary of the input parameters, the…

RISO-STATIC
Desktop

RISO-STATIC

Allows users to detect cis-regulatory modules (CRM) in genomic sequences.…

Allows users to detect cis-regulatory modules (CRM) in genomic sequences. RISO-STATIC is able to build box-links in the preprocessing phase. It only selects in output the number and the motifs of…

CompMoby
Web

CompMoby Comparative MobyDick

Identifies de novo cis-regulatory elements functioning at the transcriptional…

Identifies de novo cis-regulatory elements functioning at the transcriptional as well as the post-transcriptional level in metazoans. CompMoby is a general cis-regulatory motif discovery algorithm…

CisMiner
Desktop

CisMiner

A fuzzy-based genome-wide cis-regulatory modules (CRMs). CisMiner allows to…

A fuzzy-based genome-wide cis-regulatory modules (CRMs). CisMiner allows to perform a blind search of CRMs without any prior information about target CRMs nor limitation in the number of motifs. It…

CisPlusFinder
Desktop

CisPlusFinder

Identifies cis-regulatory modules (CRMs) independent of the information about…

Identifies cis-regulatory modules (CRMs) independent of the information about the transcription factors that regulate a target gene. CisPlusFinder may provide an accurate tool for biologists to…

LOESS
Desktop

LOESS

Characterizes and reduces the length-dependence relationship in gene…

Characterizes and reduces the length-dependence relationship in gene cis-regulatory modules (CRMs) scores. LOESS is a general and flexible approach to adjust for different dependence relations…

COMET
Web
Desktop

COMET Cluster Of Motifs E-value Tool

A method to predict the regulation of genes by transcription factors. COMET…

A method to predict the regulation of genes by transcription factors. COMET finds statistically significant clusters of motifs in a DNA sequence. The Web version of COMET allows to select motifs from…

DHC-MEGE
Desktop

DHC-MEGE DNase Hypersensitivity Connectivity Motif Enrichment in GeneExpression

A program for the identification of enriched motifs in gens found to be…

A program for the identification of enriched motifs in gens found to be differentially expressed in a microarray or RNA-seq experiment. DHC-MEGE is able to identify distal elements such as enhancers,…

CPmodule
Desktop

CPmodule

A method for finding cis-regulatory modules (CRMs) in a set of co-regulated…

A method for finding cis-regulatory modules (CRMs) in a set of co-regulated genes. CPModule can be used in a 3-phase method in which first a set of putative binding sites is computed by a motif…

MultiModule
Desktop

MultiModule

Discovers cis-regulatory modules (CRMs) and their component motifs…

Discovers cis-regulatory modules (CRMs) and their component motifs simultaneously in groups of orthologous sequences from multiple species. Compared to alignment-based motif discovery methods such as…

Genome Surveyor
Web

Genome Surveyor

Predicts transcription factor (TF) binding targets and cis-regulatory modules…

Predicts transcription factor (TF) binding targets and cis-regulatory modules (CRM), based on motifs representing experimentally determined DNA binding specificities. Genome Surveyor displays genome…

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