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Related Concept Videos

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...
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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,...
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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.
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Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

SNP discovery by transcriptome pyrosequencing.

W Brad Barbazuk1, Patrick S Schnable

  • 1Department of Biology and the Genetics Institute, University of Florida, Gainesville, FL, USA. bbarbazuk@botany.ufl.edu

Methods in Molecular Biology (Clifton, N.J.)
|March 3, 2011
PubMed
Summary
This summary is machine-generated.

High-throughput pyrosequencing efficiently discovers single nucleotide polymorphisms (SNPs) in maize. This method identified over 7,000 SNPs, advancing genetic research and breeding programs.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single nucleotide polymorphisms (SNPs) are abundant genetic variations crucial for genetic mapping, breeding, and quantitative studies.
  • Traditional Sanger sequencing is costly for deep sequencing across multiple genotypes.
  • Next-generation sequencing (NGS) technologies offer faster, more cost-effective DNA sequencing at high depths.

Purpose of the Study:

  • To discuss the application of high-throughput pyrosequencing for SNP discovery.
  • To detail the development of a computational pipeline for polymorphism detection in maize.
  • To identify putative SNPs between two maize genotypes (Mo17 and B73).

Main Methods:

  • Utilized Roche/454 Life Sciences GS-FLX Titanium Series for pyrosequencing of maize cDNA.
  • Developed a computational pipeline for analyzing sequence data and detecting polymorphisms.
  • Explored alternative strategies including Illumina short reads and reduced representation techniques.

Main Results:

  • Successfully sequenced maize cDNA using 454 pyrosequencing.
  • Identified over 7,000 putative single nucleotide polymorphisms (SNPs) between Mo17 and B73 maize.
  • Discussed data processing, visualization, and alignment strategies for SNP detection.

Conclusions:

  • High-throughput pyrosequencing is a viable and efficient method for SNP discovery in large genomes like maize.
  • The developed computational pipeline facilitates efficient polymorphism detection.
  • NGS technologies and bioinformatics tools are revolutionizing genetic research and crop improvement.