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

Bootstrapping01:24

Bootstrapping

900
The term "bootstrap" originated in the 19th century as a metaphor for self-improvement or achieving something independently, without external assistance. This concept extends to statistical bootstrapping, a self-contained method for estimating population parameters through resampling, even though it can be computationally intensive. Developed by the American statistician Dr. Bradley Efron in 1979, bootstrapping provides a robust way to perform inference when the original sample size is...
900
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

14.9K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.9K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.9K
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...
4.9K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
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...
7.2K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

12.1K
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...
12.1K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

4.3K
4.3K

You might also read

Related Articles

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

Sort by
Same author

A phage repressor involved in the DNA-damage response of <i>Francisella</i>.

PNAS nexus·2026
Same author

Parallel regulatory circuits orchestrate biofilm formation in response to c-di-GMP levels and growth phase.

PLoS genetics·2025
Same author

Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using <i>Streptomyces mirabilis</i> NRRL B-2400 in Columbia, MD.

Microbiology resource announcements·2024
Same author

Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species.

The ISME journal·2023
Same author

Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria.

Microorganisms·2023
Same author

Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity.

Viruses·2023

Related Experiment Video

Updated: Mar 14, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K

Parametric bootstrapping for biological sequence motifs.

Patrick K O'Neill1, Ivan Erill2

  • 1Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, 21250, US.

BMC Bioinformatics
|October 8, 2016
PubMed
Summary

This study introduces principled null hypotheses for analyzing biological sequence motifs, revealing that biological motifs exhibit unusual informational Gini coefficients compared to random distributions.

Keywords:
DNAInformation contentMaximum entropySampling methodsSequence motifsTranscriptional regulation

More Related Videos

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

10.8K
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.8K

Related Experiment Videos

Last Updated: Mar 14, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K
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

10.8K
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biological sequence motifs are crucial for protein-nucleic acid interactions.
  • Computational motif discovery is a central bioinformatics challenge.
  • Defining appropriate reference classes for motif comparison and effective sampling has been difficult.

Purpose of the Study:

  • To develop principled null hypotheses for sequence motifs based on information content.
  • To enable statistical analysis of motif properties by defining appropriate reference distributions.
  • To investigate global motif statistics and compare biological motifs to their null distributions.

Main Methods:

  • Defined two reference distributions: maximum entropy and truncated uniform, over motif space.
  • Derived exact sampling algorithms for these distributions.
  • Applied sampling methods to analyze prokaryotic and eukaryotic transcription factor binding site motifs.

Main Results:

  • Biological motifs, both prokaryotic and eukaryotic, show higher informational Gini coefficients (IGC) than expected by chance.
  • Developed new estimators for the motif p-value problem using maximum entropy sampling.
  • Characterized differences in global motif statistics between biological motifs and their null distributions.

Conclusions:

  • This study presents the first use of principled null hypotheses for sequence motifs based on information content.
  • Biological sequence motifs display an unusual distribution of IGC, likely due to biochemical constraints.
  • The findings provide new insights into the statistical properties of biological sequence motifs.