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Cis-regulatory Sequences

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Related Experiment Video

Updated: Apr 14, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

RSAT 2015: Regulatory Sequence Analysis Tools.

Alejandra Medina-Rivera¹, Matthieu Defrance², Olivier Sand³

¹Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada.

Nucleic Acids Research

|April 24, 2015

Summary

This summary is machine-generated.

Regulatory Sequence Analysis Tools (RSAT) is a software suite for analyzing cis-regulatory elements in genomes. It aids in motif discovery, transcription factor binding analysis, comparative genomics, and regulatory variation analysis, with new tools and reorganized servers.

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Published on: August 9, 2019

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

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Published on: May 31, 2011

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

The analysis of cis-regulatory elements is crucial for understanding gene regulation.
Existing tools for motif discovery and analysis face challenges with large-scale genomic datasets.
Advances in sequencing technologies necessitate updated and expanded bioinformatics tools.

Purpose of the Study:

To present the updated Regulatory Sequence Analysis Tools (RSAT) software suite.
To introduce new functionalities for motif discovery, transcription factor binding analysis, comparative genomics, and regulatory variation analysis.
To enhance accessibility and organization of RSAT resources for a growing number of sequenced genomes.

Main Methods:

RSAT is a modular software suite offering various analytical applications.
New programs include tools for sequence extraction, regulatory variant analysis (GWAS, population genomics), and motif clustering.
RSAT public sites are reorganized into taxon-specific servers for improved usability.
The suite is accessible via websites, web services, virtual machines, and stand-alone programs.

Main Results:

RSAT now includes 52 programs (43 previously described plus 9 new ones).
Novel tools facilitate the analysis of regulatory variants and motif clustering with visualization.
Reorganization of public sites supports analysis across an increasing number of sequenced genomes.
Comprehensive documentation, including tutorials and protocols, is available.

Conclusions:

The updated RSAT suite provides enhanced capabilities for cis-regulatory element analysis.
RSAT supports diverse applications from motif discovery to regulatory variation analysis.
The software's accessibility and documentation facilitate its use in genomic research.