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

Consensus sequence Zen.

Thomas D Schneider1

  • 1Laboratory of Experimental and Computational Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702-1201, USA. toms@ncifcrf.gov

Applied Bioinformatics
|May 8, 2004
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

Generalizing the isothermal efficiency by using Gaussian distributions.

PloS one·2023
Same author

Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences.

PloS one·2019
Same author

Elements in the λ immunity region regulate phage development: beyond the 'Genetic Switch'.

Molecular microbiology·2019
Same author

Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli.

Nucleic acids research·2019
Same author

An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment.

Journal of bacteriology·2018
Same author

Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in <i>E. coli</i>.

Frontiers in molecular biosciences·2016

Consensus sequences in molecular biology miss important genetic binding sites. Information theory offers a robust alternative, using sequence logos and walkers to quantitatively represent sequence conservation.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • Consensus sequences are a common tool in molecular biology for representing genetic sequences.
  • However, consensus sequences have significant limitations and can lead to the omission of critical biological information.
  • This can result in missed protein binding sites and unobserved biological effects.

Purpose of the Study:

  • To highlight the flaws associated with traditional consensus sequences.
  • To introduce and advocate for the use of information theory as a superior method for analyzing sequence conservation.
  • To present novel graphical representations for visualizing sequence data.

Main Methods:

  • Utilizing principles of information theory to quantitatively assess sequence conservation.

Related Experiment Videos

  • Developing and employing sequence logo graphics to represent the average conservation of multiple sites.
  • Developing and employing sequence walker graphics to represent conservation at individual genetic sites.

    • Main Results:

    • Demonstrated that information theory provides a mathematically sound framework to overcome the limitations of consensus sequences.
    • Sequence logos effectively visualize the average information content across a set of related genetic sequences.
    • Sequence walkers offer a detailed view of conservation patterns within individual sites, revealing information missed by consensus approaches.

    Conclusions:

    • Information theory-based methods, including sequence logos and walkers, offer a more accurate and comprehensive approach to analyzing genetic sequence conservation.
    • Adopting these methods can prevent the oversight of crucial binding sites and biological functions.
    • This shift from consensus sequences to information-theoretic representations enhances the precision of molecular biology studies.