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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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%...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: May 20, 2026

Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices
09:19

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Published on: March 26, 2018

A comparison of gene region simulation methods.

Audrey E Hendricks1, Josée Dupuis, Mayetri Gupta

  • 1Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America. baera@bu.edu

Plos One
|July 21, 2012
PubMed
Summary
This summary is machine-generated.

Hapgen is recommended for simulating haplotype data, accurately preserving linkage disequilibrium (LD) structure in gene regions without introducing bias. This method offers moderate sampling variation for robust association studies.

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Area of Science:

  • Population genetics
  • Bioinformatics
  • Statistical genetics

Background:

  • Accurate modeling of linkage disequilibrium (LD) in simulations is crucial for evaluating genetic association methods.
  • Limited research exists on comparing gene region simulation methods for LD structure fidelity.

Purpose of the Study:

  • To compare the accuracy of three methods (HapSim, Hapgen, haplotype resampling) in simulating LD within gene regions.
  • To assess the bias and variation introduced by each simulation approach.

Main Methods:

  • Extensive simulation study comparing pairwise LD measures and minor allele frequencies.
  • Comparison of simulated data against original HapMap data.
  • Evaluation of parameter effects on simulation quality.

Main Results:

  • HapSim simulations showed lower average LD compared to original data.
  • Hapgen and the resampling method did not introduce LD bias.
  • The resampling method exhibited minimal variation, potentially limiting generalizability.

Conclusions:

  • Hapgen is recommended for simulating replicate haplotypes from gene regions.
  • Hapgen effectively retains the unique LD structure while providing moderate sampling variation.