tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

Functional transcription factor binding site (TFBS) detection software tools | Genome annotation

Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally…
ConBind
Web

ConBind

A method to enhance alignment of short motifs, even if their mutual sequence…

A method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved transcription factor binding sites (TFBSs) by…

Master…
Desktop

Master Regulator Identification

Identifies the master regulator transcription factor in a genome. Master…

Identifies the master regulator transcription factor in a genome. Master Regulator Identification is advantageous in terms of narrowing down the search space for potential candidate transcription…

TargetOrtho
Desktop

TargetOrtho

A pipeline for the identification of transcription factor target genes.…

A pipeline for the identification of transcription factor target genes. TargetOrtho uses experimentally derived consensus-binding sites together with an alignment-free assignment of conservation.…

rVISTA
Web

rVISTA

A comparative tool for analyzing the regulatory potential of noncoding…

A comparative tool for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA…

Phyloscan
Web

Phyloscan

Combines evidence from matching sites found in orthologous data from several…

Combines evidence from matching sites found in orthologous data from several related species with evidence from multiple sites within an intergenic region, to better detect regulons. The orthologous…

Toucan
Desktop

Toucan

A Java application for the rapid discovery of significant cis-regulatory…

A Java application for the rapid discovery of significant cis-regulatory elements from sets of coexpressed or coregulated genes. Biologists can automatically (i) retrieve genes and intergenic…

RegulatorTrail
Web

RegulatorTrail

Provides a comprehensive selection of methods for the identification of…

Provides a comprehensive selection of methods for the identification of important transcriptional regulators. The web service of RegulatorTrail can be used in four distinct application scenarios to…

GPUmotif
Desktop

GPUmotif

Provides ultra-fast and energy-efficient motif analyses using graphics…

Provides ultra-fast and energy-efficient motif analyses using graphics processing units. GPUmotif proposes a ‘‘fragmentation’’ technique to hide data transfer time between memories.…

CressInt
Web

CressInt

Incorporates a variety of genome-wide data types relevant to gene regulation.…

Incorporates a variety of genome-wide data types relevant to gene regulation. CressInt is a user-friendly, freely accessible web server for integrating and analyzing genome-scale A. thaliana gene…

D2Z
Desktop

D2Z

A score for alignment-free sequence comparison. D2Z is based on comparing the…

A score for alignment-free sequence comparison. D2Z is based on comparing the frequencies of all fixed-length words in the two sequences. This method gives quadratic improvement in the time…

DISCOVER
Desktop

DISCOVER DIScriminative COnditional random field for motif recoVERy

Enjoys the dual advantage of modeling cis-regulatory modules architecture of…

Enjoys the dual advantage of modeling cis-regulatory modules architecture of sequences. DISCOVER is used in sequence analysis, most notably in gene prediction since coding regions are much better…

MEET
Desktop

MEET

A motif finding method which constructs a subspace based on the covariance of…

A motif finding method which constructs a subspace based on the covariance of numerical DNA sequences. When a candidate sequence is projected into the modeled subspace, a threshold in the Q-residuals…

ReLA
Web
Desktop

ReLA REgulatory region Local Alignment tool

A method optimized with the Smith-Waterman algorithm that identifies gene…

A method optimized with the Smith-Waterman algorithm that identifies gene regulatory regions in genomic DNA sequences through local searches of clusters of coincident transcription factor binding…

PhyloGibbs
Desktop
Web

PhyloGibbs

A motif sampling algorithm that runs on arbitrary collections of multiple local…

A motif sampling algorithm that runs on arbitrary collections of multiple local sequence alignments of orthologous sequences. The algorithm searches over all ways in which an arbitrary number of…

PhyME
Desktop

PhyME

An algorithm that integrates two important aspects of a motif's…

An algorithm that integrates two important aspects of a motif's significance - overrepresentation and cross-species conservation - into one probabilistic score. The algorithm allows the input…

cisTargetX
Web

cisTargetX

Identifies the correct motif from a set of co-expressed genes and predicts…

Identifies the correct motif from a set of co-expressed genes and predicts target genes of individual Transcription Factors (TFs). cisTargetX uses statistical correlations between co-expressed gene…

ConSite
Web

ConSite

A graphical, web-based interface for computer-assisted prediction of regulatory…

A graphical, web-based interface for computer-assisted prediction of regulatory regions in higher eukaryotes, powered by cross-species comparison. Besides the intuitive interface design, ConSite…

BLISS
Web

BLISS

A web-based application for identifying conserved regulatory modules in…

A web-based application for identifying conserved regulatory modules in distantly related orthologous sequences. Unlike existing approaches, it performs the cross-genome comparison at the binding…

Related Websites
Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.