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

2SNP: scalable phasing based on 2-SNP haplotypes.

Dumitru Brinza1, Alexander Zelikovsky

  • 1Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA.

Bioinformatics (Oxford, England)
|November 17, 2005
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

<i>Special Issue:</i> 13th International Conference on Computational Advances in Bio and Medical Sciences.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

The influence of diabetes mellitus on blood vessels' amounts and immune status in case of breast cancer.

Romanian journal of morphology and embryology = Revue roumaine de morphologie et embryologie·2025
Same author

Estimating Enzyme Expression and Metabolic Pathway Activity in <i>Borreliella</i>-Infected and Uninfected Mice.

Journal of computational biology : a journal of computational molecular cell biology·2024
Same author

<i>Special Issue, Part I</i> 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022).

Journal of computational biology : a journal of computational molecular cell biology·2023
Same author

Assessing the Resilience of Machine Learning Classification Algorithms on SARS-CoV-2 Genome Sequences Generated with Long-Read Specific Errors.

Biomolecules·2023
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

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

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

The 2SNP software offers a rapid and scalable algorithm for haplotype inference, significantly outperforming existing methods like GERBIL and PHASE in speed and accuracy for large-scale genome sequencing data.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Haplotype inference is crucial for understanding genetic variation and disease association.
  • Existing algorithms for haplotype phasing can be computationally intensive, limiting their application to large datasets.

Purpose of the Study:

  • To introduce 2SNP, a novel software package for fast and accurate haplotype inference.
  • To evaluate the performance of 2SNP against established methods using real-world genomic data.

Main Methods:

  • Implementation of a fast, scalable algorithm for haplotype inference using pairwise SNP genotype statistics.
  • Input: genotype matrix; Output: haplotype matrix.
  • Testing on HapMap datasets across 79 regions.

Related Experiment Videos

Main Results:

  • 2SNP demonstrated several orders of magnitude improvement in speed compared to GERBIL and PHASE.
  • The accuracy of 2SNP, measured by correctly phased genotypes and error rates, was comparable to GERBIL and PHASE.
  • Phasing 30 genotypes with 1381 SNPs took 41 seconds with 2SNP, versus over a week for GERBIL and PHASE.

Conclusions:

  • 2SNP provides a highly efficient and accurate solution for haplotype phasing of large genomic datasets.
  • The software is suitable for analyzing data from sources like DNA arrays.
  • 2SNP represents a significant advancement in computational genomics tools.