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 Experiment Videos

FootPrinter: A program designed for phylogenetic footprinting.

Mathieu Blanchette1, Martin Tompa

  • 1Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA.

Nucleic Acids Research
|June 26, 2003
PubMed
Summary
This summary is machine-generated.

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

Graphylo Var: Predicting the impact of non-coding variants using a multi-species sequence model.

Bioinformatics (Oxford, England)·2026
Same author

H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs.

Nature genetics·2026
Same author

Telomere-to-telomere assembly detects genomic diversity in Canadian strains of Borrelia burgdorferi.

Cell reports·2026
Same author

A multivariate approach to identify association between peripheral blood DNA methylation and cerebrospinal fluid biomarkers of Alzheimer disease.

Scientific reports·2025
Same author

RobusTAD: reference panel based annotation of nested topologically associating domains.

Genome biology·2025
Same author

R3Design: deep tertiary structure-based RNA sequence design and beyond.

Briefings in bioinformatics·2024
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Phylogenetic footprinting identifies regulatory elements by finding conserved motifs in homologous DNA sequences across species. New software, FootPrinter, enhances this discovery using phylogenetic relationships for more accurate predictions.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenetic footprinting is a computational method for identifying conserved regulatory elements.
  • It relies on comparing homologous DNA sequences from related species.
  • Discovering regulatory elements is crucial for understanding gene regulation.

Purpose of the Study:

  • To introduce novel web software for phylogenetic footprinting.
  • To improve the accuracy of regulatory element discovery by incorporating phylogenetic information.
  • To provide researchers with a user-friendly tool for analyzing homologous regulatory regions.

Main Methods:

  • The study describes a web-based software tool named FootPrinter.
  • The software utilizes phylogenetic relationships among homologous sequences.

Related Experiment Videos

  • It identifies conserved motifs within these sequences to predict regulatory elements.

    • Main Results:

    • The FootPrinter software is designed for accurate prediction of regulatory elements.
    • It leverages evolutionary information from multiple species.
    • The tool aims to enhance the efficiency of motif discovery in comparative genomics.

    Conclusions:

    • FootPrinter offers an advanced approach to phylogenetic footprinting.
    • The software facilitates the discovery of functional regulatory elements.
    • It is available online for the research community.