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

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Pleiotropy01:33

Pleiotropy

Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
Hardy-Weinberg Principle01:49

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...
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...
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%...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

You might also read

Related Articles

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

Sort by
Same author

Differential quantification of alternative splicing events on spliced pangenome graphs.

PLoS computational biology·2024
Same author

PangeBlocks: customized construction of pangenome graphs via maximal blocks.

BMC bioinformatics·2024
Same author

Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development.

bioRxiv : the preprint server for biology·2024
Same author

Data Structures for SMEM-Finding in the PBWT.

International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)·2024
Same author

RecGraph: recombination-aware alignment of sequences to variation graphs.

Bioinformatics (Oxford, England)·2024
Same author

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.

Bioinformatics (Oxford, England)·2023

Related Experiment Video

Updated: Jun 12, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Pure parsimony xor haplotyping.

Paola Bonizzoni1, Gianluca Della Vedova, Riccardo Dondi

  • 1Dipartimento di Informatica, Sistemistica e Comunicazione, Università Degli Studi di Milano-Bicocca, Viale Sarca 336, Milano 20126, Italy. bonizzoni@disco.unimib.it

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|May 26, 2010
PubMed
Summary

This study introduces a new method for haplotype resolution using xor-genotype data, offering efficient algorithms and a k-approximation for genetic studies. The approach scales to large datasets, aiding genetic research.

More Related Videos

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

Related Experiment Videos

Last Updated: Jun 12, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

Area of Science:

  • Computational Biology
  • Genetics
  • Bioinformatics

Background:

  • Haplotype resolution is crucial for genetic studies.
  • Xor-genotype data offers a cost-effective alternative to traditional methods.
  • Existing methods for xor-genotype data are limited.

Purpose of the Study:

  • To formulate haplotype resolution from xor-genotype data using pure parsimony.
  • To develop efficient algorithms for solving this problem.
  • To evaluate the scalability and accuracy of the proposed methods.

Main Methods:

  • Formulation based on pure parsimony model.
  • Development of polynomial-time algorithms for restricted cases.
  • Fixed-parameter tractable algorithm for the general case.
  • Graph representation and combinatorial properties analysis.
  • Polynomial-time k-approximation algorithm.
  • Heuristic approach and experimental analysis.

Main Results:

  • Exact solutions achieved for specific cases.
  • Efficient algorithms developed for general and restricted scenarios.
  • Demonstrated polynomial-time k-approximation.
  • Heuristic shows scalability on large, real-world datasets (HapMap).

Conclusions:

  • The pure parsimony formulation provides an effective framework for haplotype resolution from xor-genotype data.
  • The developed algorithms offer computational efficiency for genetic studies.
  • The heuristic approach is suitable for large-scale genomic data analysis.