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

How well does the HoT score reflect sequence alignment accuracy?

Barry G Hall1

  • 1Bellingham Research Institute. barryhall@zeninternet.com

Molecular Biology and Evolution
|May 7, 2008
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

Building Phylogenetic Trees From Genome Sequences With kSNP4.

Molecular biology and evolution·2023
Same author

Estimating microbial population data from optical density.

PloS one·2022
Same author

Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP.

Cladistics : the international journal of the Willi Hennig Society·2021
Same author

Stress proteins as predictors of COVID-19 outcomes.

Cell stress & chaperones·2021
Same author

Statistical Package for Growth Rates Made Easy.

Molecular biology and evolution·2017
Same author

Population Dynamics of Staphylococcus aureus in Cystic Fibrosis Patients To Determine Transmission Events by Use of Whole-Genome Sequencing.

Journal of clinical microbiology·2017
Same journal

The life history of recessive deleterious alleles as seen through the eyes of a honey bee (Apis mellifera).

Molecular biology and evolution·2026
Same journal

Severe bottleneck of ancient Homo populations: Insights from computational modeling and relevant fossil evidence.

Molecular biology and evolution·2026
Same journal

Population Epigenetics: Deciphering DNA Methylation Diversity and its Implications for Health, Disease, and Evolution.

Molecular biology and evolution·2026
Same journal

Genomic signature of repeated transitions to diurnality in spiders.

Molecular biology and evolution·2026
Same journal

Phylogenomic blind spots: The limits of UCE and BUSCO loci in the presence of gene flow.

Molecular biology and evolution·2026
Same journal

seqLens: Optimizing Language Models for Genomic Predictions.

Molecular biology and evolution·2026
See all related articles

The Heads or Tails (HoT) method checks multiple sequence alignment consistency. Higher HoT scores correlate with better alignment accuracy, but may overestimate true accuracy depending on the alignment method used.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Multiple sequence alignment (MSA) is crucial for biological research, impacting downstream analyses like phylogenetics and motif discovery.
  • The Heads or Tails (HoT) method provides a reliability check for MSAs by comparing alignments of original and reverse-complemented sequences.
  • Alignment accuracy directly influences the reliability of biological interpretations and applications.

Purpose of the Study:

  • To evaluate the correlation between Heads or Tails (HoT) scores and the actual accuracy of multiple sequence alignments.
  • To determine if HoT scores can reliably predict alignment quality across different alignment methodologies.
  • To assess the extent to which HoT scores might overestimate alignment accuracy.

Main Methods:

Related Experiment Videos

  • Utilized the Heads or Tails (HoT) method to assess the consistency of multiple sequence alignments.
  • Compared HoT scores generated from alignments with established measures of alignment accuracy.
  • Analyzed the impact of different multiple sequence alignment algorithms on HoT score reliability.

Main Results:

  • A positive correlation was observed between HoT scores and alignment accuracy, indicating higher HoT scores suggest better alignments.
  • HoT scores generally overestimate the true accuracy of multiple sequence alignments.
  • The degree of overestimation varied depending on the specific multiple sequence alignment method employed.

Conclusions:

  • Alignments with higher HoT scores are generally preferable due to their positive correlation with accuracy.
  • Caution is advised as HoT scores can overestimate alignment accuracy.
  • The reliability of HoT scores as a measure of alignment quality is dependent on the underlying MSA method.