Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Gene expression profiling of dendritic cell tolerance dysfunction in women with systemic lupus erythematosus.

Frontiers in immunology·2026
Same author

Training biologists in Unix command-line skills: From curriculum to interactive online tutorials.

PLoS computational biology·2026
Same author

Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities.

F1000Research·2026
Same author

Web-Based Discovery of Regulatory Motifs in Non-model Plants.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

A low-level Cdkn1c/p57<sup>kip2</sup> expression in spinal progenitors drives the transition from proliferative to neurogenic modes of division.

EMBO reports·2025
Same author

AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow.

Bioinformatics (Oxford, England)·2025
Same journal

iMUT-seq mapping of DSB-induced mutations with high sensitivity at single-nucleotide resolution.

Nature protocols·2026
Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026
Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026
Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026
Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026
Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026
See all related articles

Related Experiment Video

Updated: Jun 30, 2026

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology
09:39

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology

Published on: March 31, 2022

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.

Olivier Sand1, Morgane Thomas-Chollier, Eric Vervisch

  • 1Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, Belgium.

Nature Protocols
|September 20, 2008
PubMed
Summary
This summary is machine-generated.

This protocol automates the analysis of multiple datasets using the Regulatory Sequence Analysis Tools (RSAT) web services. It enables discovery of cis-acting elements and transcription factor binding motifs in gene promoters.

More Related Videos

Fixed Target Serial Data Collection at Diamond Light Source
06:19

Fixed Target Serial Data Collection at Diamond Light Source

Published on: February 26, 2021

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Related Experiment Videos

Last Updated: Jun 30, 2026

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology
09:39

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology

Published on: March 31, 2022

Fixed Target Serial Data Collection at Diamond Light Source
06:19

Fixed Target Serial Data Collection at Diamond Light Source

Published on: February 26, 2021

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Automating biological data analysis is crucial for handling large datasets.
  • Regulatory Sequence Analysis Tools (RSAT) offer valuable bioinformatics resources.
  • Programmatic access to web services enhances workflow efficiency.

Purpose of the Study:

  • To describe a protocol for programmatic access to RSAT web services.
  • To automate the discovery of cis-acting elements in gene promoters.
  • To apply this workflow to identify transcription factor binding motifs.

Main Methods:

  • Developing a Perl client to connect to RSAT web services.
  • Implementing a workflow for analyzing gene cluster promoters.
  • Utilizing ChIP-chip data to identify target genes.

Main Results:

  • Successful prediction of transcription factor binding motifs.
  • Detection of significantly overrepresented hexanucleotides in promoter regions.
  • Generation of feature maps illustrating putative binding site locations.

Conclusions:

  • The protocol provides an automated method for cis-acting element discovery.
  • This approach is effective for analyzing transcription factor binding sites.
  • The method is suitable for bioinformaticians and biologists with Perl programming skills.