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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Sanger Sequencing01:57

Sanger Sequencing

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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Jun 15, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Repeat subtraction-mediated sequence capture from a complex genome.

Yan Fu1, Nathan M Springer, Daniel J Gerhardt

  • 1Department of Agronomy, Iowa State University, Ames, IA 50011, USA.

The Plant Journal : for Cell and Molecular Biology
|March 17, 2010
PubMed
Summary
This summary is machine-generated.

A new blocker-free sequence capture method simplifies genomic resequencing. This approach efficiently targets specific DNA regions, enabling accurate SNP discovery and novel sequence recovery across species.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Sequence capture technologies are crucial for targeted genomic resequencing.
  • Existing protocols often require large quantities of blocking DNA, posing production challenges.
  • Developing blocker-free methods is essential for streamlined genomic analysis.

Purpose of the Study:

  • To develop and evaluate a novel, blocker-free, two-stage sequence capture protocol.
  • To assess the efficiency of this method for resequencing large genomic intervals and dispersed genes.
  • To determine its utility for single nucleotide polymorphism (SNP) discovery and novel sequence recovery.

Main Methods:

  • Utilized NimbleGen arrays for a two-stage capture process.
  • First stage: depletion of repetitive sequences from the DNA library.
  • Second stage: enrichment of targeted genomic loci.

Main Results:

  • Successfully resequenced non-repetitive regions of a 2.2 Mb chromosomal interval and 43 maize genes.
  • Achieved substantial enrichment (1800-3000-fold) and high target base coverage (80-98%).
  • Identified over 2500 SNPs with low false-positive rates, even with paralogous sequences, and recovered novel non-reference alleles.

Conclusions:

  • The developed blocker-free, two-stage capture protocol is highly efficient for targeted genomic resequencing.
  • This method facilitates accurate SNP identification and the recovery of novel genetic variations.
  • The technology's adaptability through custom array design makes it broadly applicable across diverse species.