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

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...
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
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...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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...
Wilcoxon Signed-Ranks Test for Matched Pairs01:09

Wilcoxon Signed-Ranks Test for Matched Pairs

The Wilcoxon signed-rank test for matched pairs evaluates the null hypothesis by combining the ranks of differences with their signs. It essentially tests whether the median of the differences in a population of matched pairs is zero. Since the test incorporates more information than the sign test, it generally yields more trustable conclusions. This test also does not require the data to follow a normal distribution, but two conditions must be met for it to be applicable: (1) the data must...

You might also read

Related Articles

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

Sort by
Same author

Lethal conflict after group fission in wild chimpanzees.

Science (New York, N.Y.)·2026
Same author

Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.

Current protocols·2026
Same author

Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.

Genome biology·2026
Same author

A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets.

Current protocols·2026
Same author

Correction: Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations.

PLoS computational biology·2026
Same author

ViTrace detects viral signatures in tumor transcriptomes using a hybrid language model.

Communications biology·2025
Same journal

The male-biased sex ratio in humans and its role in the transition from promiscuity to pair bonding.

Journal of theoretical biology·2026
Same journal

Quantifying the counter-intuitive effects of vaccination by coupling the transmission dynamics of COVID-19 and the evolution of human behaviors.

Journal of theoretical biology·2026
Same journal

An integrative model of FGF2-induced signaling and muscle cell proliferation.

Journal of theoretical biology·2026
Same journal

A hybrid reaction-diffusion and mechanical stimulus model for mandibular bone remodeling under chewing and vibratory loading.

Journal of theoretical biology·2026
Same journal

Integrated tick management strategies in fragmented peridomestic environments.

Journal of theoretical biology·2026
Same journal

Joint likelihood-free inference of the number of selected single nucleotide polymorphisms and their selection coefficients in an evolving population.

Journal of theoretical biology·2026
See all related articles

Related Experiment Video

Updated: May 31, 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

New powerful statistics for alignment-free sequence comparison under a pattern transfer model.

Xuemei Liu1, Lin Wan, Jing Li

  • 1School of Physics, South China University of Technology, Guangzhou, PR China.

Journal of Theoretical Biology
|July 5, 2011
PubMed
Summary
This summary is machine-generated.

New alignment-free sequence comparison statistics improve gene comparison power. These novel methods, based on local sequence pairs, offer enhanced accuracy for identifying gene regulatory regions and horizontally transferred genes.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: May 31, 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

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Alignment-free sequence comparison is crucial for analyzing gene regulatory regions and detecting horizontal gene transfer.
  • Existing methods like D2, D*2, and D(s)2 have limitations, with their statistical power approaching a sub-optimal limit for long sequences under pattern transfer models.

Purpose of the Study:

  • To develop novel alignment-free sequence comparison statistics with enhanced power.
  • To improve the accuracy and reliability of gene regulatory region comparison and horizontal gene transfer identification.

Main Methods:

  • Developed new statistics by adapting D2, D*2, and D(s)2 to compare local sequence pairs.
  • Summed comparisons across all local sequence pairs of a defined length.
  • Evaluated statistical power under a pattern transfer model.

Main Results:

  • The newly developed statistics demonstrate significantly greater power compared to their original counterparts.
  • The enhanced statistics show a tendency towards a power limit of 1 as sequence length increases, outperforming previous approaches.

Conclusions:

  • The novel alignment-free statistics offer a substantial improvement in sequence comparison power.
  • These enhanced methods provide a more robust tool for genomic analyses, particularly in comparing gene regulatory regions and identifying horizontally transferred genes.