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

FootPrinter3: phylogenetic footprinting in partially alignable sequences.

Fei Fang1, Mathieu Blanchette

  • 1McGill Centre for Bioinformatics, 3775 University St, Montréal, Québec, Canada, H3A 2B4.

Nucleic Acids Research
|July 18, 2006
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

Application and efficacy evaluation of a novel electrolytic water-disinfecting toilet for infection prevention and control in healthcare facility restrooms.

Frontiers in public health·2026
Same author

GraphyloVar: predicting the impact of non-coding variants using a multi-species sequence model.

Bioinformatics (Oxford, England)·2026
Same author

Integrated top-down and bottom-up proteomics enables precise characterization of proteoforms within the protein corona.

Nature communications·2026
Same author

Multiple exposure sources and occupational fatigue profiles among healthcare workers: a cross-sectional latent profile analysis.

Frontiers in public health·2026
Same author

The dissonance of "expectation-reality": a narrative study on preoperative identity expectations and postoperative identity reconstruction of patients after metabolic and bariatric surgery.

Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery·2026
Same author

Missed diagnosis of pelvic organ prolapse complicated with cervical cancer: a retrospective case series of five patients and review of literature.

Gynecology and pelvic medicine·2026

FootPrinter3 predicts transcription factor binding sites using phylogenetic footprinting. This new web server integrates alignment and motif discovery for improved accuracy across diverse species.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenetic footprinting is crucial for identifying regulatory elements in genomes.
  • Existing methods rely on either multiple sequence alignment or motif discovery, each with limitations.

Purpose of the Study:

  • To develop an integrated web server, FootPrinter3, for enhanced transcription factor binding site prediction.
  • To combine the strengths of alignment-based and motif-based phylogenetic footprinting approaches.

Main Methods:

  • FootPrinter3 utilizes local multiple sequence alignment blocks where available and reliable.
  • It also identifies motifs in unalignable genomic regions, accommodating sequence divergence.
  • The approach integrates alignment-based specificity with motif-based sensitivity.

Related Experiment Videos

Main Results:

  • FootPrinter3 provides accurate transcription factor binding site predictions.
  • The tool effectively leverages sequences from both closely related and highly diverged species.
  • It offers improved sensitivity in the presence of highly diverged species compared to previous methods.

Conclusions:

  • FootPrinter3 is a valuable tool for analyzing large-scale genomic data, particularly vertebrate genomes.
  • The integrated approach enhances the prediction of regulatory elements.
  • It facilitates the exploitation of diverse genomic sequences for biological discovery.