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

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

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

Sort by
Same author

New causal discovery algorithm over censored variables identifies subtype-specific drivers of breast cancer progression.

GigaScience·2026
Same author

Trio-based GWAS reveals novel loci associated with different forms of isolated cleft lip.

medRxiv : the preprint server for health sciences·2026
Same author

Neoadjuvant Radiation is Causally Linked to Increased Operative Time and Perioperative Blood Transfusion in Pancreatic Ductal Adenocarcinoma.

The Journal of surgical research·2026
Same author

Chromatin architecture and physical constriction cooperate in phenotype switching and cancer cell dissemination.

bioRxiv : the preprint server for biology·2026
Same author

Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications.

CHEST pulmonary·2026
Same author

Microbial lung-to-blood translocation associates with systemic inflammation in severe pneumonia: evidence from paired plasma and lower respiratory tract metagenomics.

Intensive care medicine experimental·2026

Related Experiment Video

Updated: Jul 10, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Web-based identification of evolutionary conserved DNA cis-regulatory elements.

Panayiotis V Benos1, David L Corcoran, Eleanor Feingold

  • 1Department of Computational Biology, University of Pittsburgh School of Medicine, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 13, 2007
PubMed
Summary
This summary is machine-generated.

FOOTER is a computational tool that uses phylogenetic footprinting to identify transcription factor binding sites by analyzing conserved sequences across species. This method enhances accuracy by leveraging evolutionary information to distinguish true binding sites from genomic noise.

More Related Videos

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

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

Published on: October 5, 2018

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Related Experiment Videos

Last Updated: Jul 10, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

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

Published on: October 5, 2018

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transcription factors regulate gene expression by binding to specific DNA sequences.
  • Identifying transcription factor binding sites computationally is challenging due to short, degenerate DNA patterns and genomic noise.
  • Evolutionary conservation provides a powerful approach to enhance the detection of functional DNA elements.

Purpose of the Study:

  • To introduce FOOTER, a web-based algorithm for quantitative evaluation of mammalian transcription factor binding sites.
  • To utilize phylogenetic footprinting to improve the signal-to-noise ratio in transcription factor binding site prediction.
  • To provide users with a tool for analyzing human and mouse promoter sequences for conserved transcription factor binding sites.

Main Methods:

  • Development of the FOOTER algorithm based on the phylogenetic footprinting concept.
  • Comparative analysis of human and mouse promoter sequences.
  • Quantitative evaluation of putative transcription factor binding sites using evolutionary conservation information.

Main Results:

  • FOOTER successfully identifies conserved transcription factor binding sites by analyzing sequence alignments.
  • The tool provides visualizations of sequence conservation and predicts single-nucleotide polymorphisms near binding sites.
  • The method effectively overcomes the challenge of low signal-to-noise ratio in computational binding site prediction.

Conclusions:

  • Phylogenetic footprinting is a robust strategy for identifying transcription factor binding sites.
  • FOOTER offers a valuable web-based resource for researchers studying gene regulation and comparative genomics.
  • The tool aids in understanding the functional significance of conserved sequences and their association with genetic variations.