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

Calculating the SNP-effective sample size from an alignment.

Bernhard Haubold1, Thomas Wiehe

  • 1Max-Planck-Institut für Chemische Okologie, Carl-Zeiss-Promenade 10, D-07745 Jena, Germany.

Bioinformatics (Oxford, England)
|February 12, 2002
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

Muller's ratchet and gene duplication.

Theoretical population biology·2025
Same author

Fast detection of unique genomic regions.

Computational and structural biotechnology journal·2025
Same author

Detection and annotation of unique regions in mammalian genomes.

G3 (Bethesda, Md.)·2024
Same author

Detecting adaptive changes in gene copy number distribution accompanying the human out-of-Africa expansion.

Human genome variation·2024
Same author

Marker discovery in the large.

Bioinformatics advances·2024
Same author

Copy number variation and population-specific immune genes in the model vertebrate zebrafish.

eLife·2024
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Calculating the effective sample size (n(eff)) for DNA sequence alignments is crucial. Our method reveals that n(eff) is often much smaller than expected due to uneven sequence coverage in BLAST results.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The number of detectable Single Nucleotide Polymorphisms (SNPs) depends on sequence alignment length and sample size.
  • Uneven sequence coverage in typical alignments (e.g., BLAST searches against EST databases) obscures the true sample size.

Purpose of the Study:

  • To develop a method for calculating the effective sample size (n(eff)) in BLAST sequence alignments.
  • To address the challenge of determining accurate sample sizes with non-uniform sequence coverage.

Main Methods:

  • Developed a novel method to compute the effective sample size (n(eff)) for sequence alignments.
  • Accounted for the logarithmic contribution of multiple sequence coverage to SNP yield.

Main Results:

Related Experiment Videos

  • The effective sample size (n(eff)) is often significantly smaller than the apparent sample size.
  • Demonstrated this finding with two illustrative examples of typical sequence alignments.

Conclusions:

  • The proposed method provides a more accurate estimation of sample size for SNP detection in sequence alignments.
  • Highlights the importance of considering effective sample size for reliable genomic analyses.