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

Position-effect Variegation02:32

Position-effect Variegation

6.4K
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
6.4K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.3K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.3K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

56
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
56
Sanger Sequencing01:57

Sanger Sequencing

755.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
755.1K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.8K
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%...
17.8K
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

99
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...
99

You might also read

Related Articles

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

Sort by
Same author

RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.

Bioinformatics (Oxford, England)·2026
Same author

Vision transformer autoencoders captures local and non-local features in brain imaging to reveal novel genetic associations.

Communications biology·2026
Same author

Replicability of unsupervised deep learning derived image phenotypes.

bioRxiv : the preprint server for biology·2026
Same author

Genetic architecture of white matter microstructure captured by unsupervised deep representation learning of fractional anisotropy maps.

Nature communications·2026
Same author

Improving Vancomycin Therapeutic Drug Monitoring With a Deep Learning-Based Two-Compartment Predictive Model: Development and Validation Study.

JMIR AI·2026
Same author

HiFiMAP: High-resolution fast identity-by-descent mapping test.

medRxiv : the preprint server for health sciences·2026

Related Experiment Video

Updated: Jul 26, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.2K

Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model.

Ahsan Sanaullah1, Degui Zhi2, Shaojie Zhang3

  • 1Department of Computer Science, University of Central Florida, Orlando, Florida 32816, USA.

Genome Research
|June 14, 2023
PubMed
Summary

We introduce a new method, minimal positional substring cover (MPSC), for haplotype reconstruction in large biobank-scale panels. This approach offers efficient haplotype threading and improves genotype imputation by revealing data characteristics.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.3K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.3K

Related Experiment Videos

Last Updated: Jul 26, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.2K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.3K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.3K

Area of Science:

  • Genetics
  • Computational Biology
  • Bioinformatics

Background:

  • The Li and Stephens (LS) hidden Markov model (HMM) is effective for haplotype reconstruction but inefficient for large reference panels due to linear time complexity.
  • The Patterned Binary Search Tree (PBWT) offers a faster approach for LS HMM by efficiently identifying local haplotype matches.

Purpose of the Study:

  • To present new findings on the solution space of the minimal positional substring cover (MPSC) problem.
  • To develop optimal algorithms for MPSC, including enumeration, length-maximal, and h-MPSC solutions.
  • To reveal the solution space of the LS model for large-scale panels and improve genotype imputation.

Main Methods:

  • Formulated haplotype reconstruction as the minimal positional substring cover (MPSC) problem.
  • Developed optimal algorithms for MPSC, including solution enumeration and variations like length-maximal and h-MPSC.
  • Analyzed the solution space of MPSC for large biobank-scale panels.

Main Results:

  • The MPSC formulation enables haplotype threading with time complexity constant to sample size (O(N)), making it feasible for large panels.
  • New algorithms provide insights into the MPSC solution space and reveal characteristics of biobank-scale datasets.
  • The proposed method demonstrates potential for improving genotype imputation accuracy.

Conclusions:

  • The MPSC problem offers a scalable alternative to the LS HMM for haplotype reconstruction in large datasets.
  • Developed algorithms effectively explore the MPSC solution space and provide valuable insights into genetic data.
  • This approach enhances genotype imputation and aids in understanding large-scale genomic data characteristics.