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

Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Phylogenetic Species Concept in Microbiology01:22

Phylogenetic Species Concept in Microbiology

The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...

You might also read

Related Articles

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

Sort by
Same author

Promoting the Mathematization of Physics: Hermann Minkowski's Draft Presentations of His 1908 "Grundgleichungen" Paper.

Berichte zur Wissenschaftsgeschichte·2026
Same author

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture.

Nature microbiology·2026
Same author

From orbits to orbitals. Early pictorializations of electron probability densities.

Annals of science·2025
Same author

High-Throughput Profiling of Colorectal Cancer Liver Metastases Reveals Intra- and Inter-Patient Heterogeneity in the EGFR and WNT Pathways Associated with Clinical Outcome.

Cancers·2022
Same author

Annotation survey and life cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit.

Fungal genetics and biology : FG & B·2022
Same author

Editorial: Gene Regulation as a Driver of Adaptation and Speciation.

Frontiers in genetics·2021

Related Experiment Video

Updated: Jun 30, 2026

Spotting Cheetahs: Identifying Individuals by Their Footprints
09:47

Spotting Cheetahs: Identifying Individuals by Their Footprints

Published on: May 1, 2016

Evaluating phylogenetic footprinting for human-rodent comparisons.

Tilman Sauer1, Ekaterina Shelest, Edgar Wingender

  • 1Department of Bioinformatics, UKG, Georg-August-University of Goettingen Goldschmidtstrasse 1, 37077 Goettingen, Germany. tsa@bioinf.med.uni-goettingen.de

Bioinformatics (Oxford, England)
|December 8, 2005
PubMed
Summary

Phylogenetic footprinting effectively identifies conserved transcription factor binding sites (TFBSs) across species. A 65% sequence identity threshold captures 72% of known TFBSs, though some TFBSs show pattern rather than strict sequence conservation.

More Related Videos

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Related Experiment Videos

Last Updated: Jun 30, 2026

Spotting Cheetahs: Identifying Individuals by Their Footprints
09:47

Spotting Cheetahs: Identifying Individuals by Their Footprints

Published on: May 1, 2016

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic footprinting leverages alignments of non-coding orthologous regions to identify regulatory elements and transcription factor binding sites (TFBSs).
  • A systematic evaluation is crucial for optimizing its application in discovering novel TFBSs.

Purpose of the Study:

  • To systematically evaluate the validity and usability of phylogenetic footprinting for identifying transcription factor binding sites (TFBSs).
  • To determine optimal parameters for effective TFBS identification using cross-species comparisons.

Main Methods:

  • Utilized 2678 human, mouse, and rat TFBSs from the TRANSFAC database.
  • Combined gene annotation and sequence homology searches to ensure orthologous sequence retrieval.
  • Evaluated the impact of sequence identity thresholds and alignment algorithms on TFBS identification.

Main Results:

  • A sequence identity threshold of at least 65% proved most effective in distinguishing TFBSs from non-functional sequences.
  • Approximately 72% of known TFBSs were found to be conserved using this threshold in human-rodent comparisons.
  • Conservation levels varied significantly across different transcription factors and depended on the regulated gene's function.
  • Some TFBSs exhibited high pattern conservation rather than strict sequence conservation, indicating limitations of purely sequence-based methods.

Conclusions:

  • Phylogenetic footprinting, particularly with a 65% sequence identity threshold, is a valuable tool for identifying conserved TFBSs.
  • The effectiveness of sequence conservation varies, and pattern conservation should also be considered for a comprehensive analysis.
  • This study provides empirical data to refine the application of phylogenetic footprinting in regulatory genomics.