Links tagged with 'transcriptional regulatory elements'

Found 20 links

Displaying 15 links

CEASTool Content

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Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
CEAS: cis-regulatory element annotation system200673

DiRETool Content

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A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.

FlyFactorSurveyDatabase Content

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FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

Genome SurveyorTool Content

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Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila20113

MEME SuiteTool Content

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The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

MoD ToolsTool Content

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Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

REDflyDatabase Content

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The REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both causal and power users and is intended as a tool for facilitating computational as well as experimental studies of transcriptional regulation.

This content is being maintained by halfon.

REDflyDatabase Content

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Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct.

This content is being maintained by halfon.

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