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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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 DNA...
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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...

You might also read

Related Articles

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

Sort by
Same author

Incorporation of clinical and molecular variant properties improves the performance of in silico pathogenicity prediction tools.

Genetics in medicine : official journal of the American College of Medical Genetics·2026
Same author

Farm animal evolution demonstrates hidden molecular basis of human traits.

bioRxiv : the preprint server for biology·2026
Same author

Hotspots of human mutation point to clonal expansions in spermatogonia.

Nature·2025
Same author

Systematic analysis of snRNA genes reveals frequent <i>RNU2-2</i> variants in dominant and recessive developmental and epileptic encephalopathies.

medRxiv : the preprint server for health sciences·2025
Same author

Hotspots of human mutation point to clonal expansions in spermatogonia.

medRxiv : the preprint server for health sciences·2025
Same author

Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.

Plant & cell physiology·2024

Related Experiment Video

Updated: Jul 8, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Analysis of sequence conservation at nucleotide resolution.

Saurabh Asthana1, Mikhail Roytberg, John Stamatoyannopoulos

  • 1Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.

Plos Computational Biology
|January 2, 2008
PubMed
Summary

This study introduces a novel method, Sequence CONservation Evaluation (SCONE), to score evolutionary conservation at single nucleotide resolution. SCONE reveals that many functionally important conserved sites are fragmented and outside previously identified conserved regions.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
18:10

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Related Experiment Videos

Last Updated: Jul 8, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
18:10

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Understanding evolutionary history and selective pressure on the human genome is crucial for identifying functional elements and genetic variation.
  • Existing methods for sequence conservation analysis focus on large regions, potentially missing smaller, functionally significant sites.
  • Nucleotide-level conservation analysis is vital for predicting functional significance and analyzing regulatory sequences.

Purpose of the Study:

  • To develop a novel computational approach for scoring evolutionary conservation at individual base-pair resolution.
  • To assess the functional significance of conserved nucleotides, particularly in noncoding regions.
  • To investigate the distribution of conserved nucleotides within functional genomic regions.

Main Methods:

  • Developed a novel computational approach to estimate evolutionary rates and compute neutrality probabilities at nucleotide resolution.
  • Generated Sequence CONservation Evaluation (SCONE) scores across a portion of the human genome using data from up to 23 species.
  • Correlated SCONE scores with human polymorphism allele frequencies in coding and noncoding regions.

Main Results:

  • SCONE scores show a clear correlation with human polymorphism allele frequencies in both coding and noncoding DNA.
  • The majority of conserved noncoding nucleotides are found outside of long conserved elements and are under ongoing selection in humans.
  • Functionally important conserved positions are often fragmented, appearing as individual sites or short conserved sequences (<15 bp), rather than large blocks.

Conclusions:

  • The novel SCONE method provides nucleotide-level resolution for evolutionary conservation analysis.
  • Functionally important conserved sites, especially in noncoding DNA, are frequently fragmented and reside outside of traditionally defined conserved regions.
  • These fragmented conserved sites are experiencing selection in modern human populations and are critical for understanding genome function.