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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,...
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...

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Related Experiment Video

Updated: Jun 23, 2026

An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants
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Single nucleotide polymorphism discovery in barley using autoSNPdb.

Chris Duran1, Nikki Appleby, Megan Vardy

  • 1Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia.

Plant Biotechnology Journal
|April 24, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces autoSNPdb, a database for identifying single nucleotide polymorphisms (SNPs) in any species using sequence data. It provides valuable genetic variation information, aiding in genotype-phenotype linkage and diversity assessment.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Molecular markers are crucial for linking genotype to phenotype, constructing genetic maps, and assessing genetic diversity.
  • Single nucleotide polymorphisms (SNPs) are the most common molecular genetic markers, but accurate identification from sequence data is challenging.
  • Existing methods require careful validation to distinguish true genetic variation from DNA sequencing errors.

Purpose of the Study:

  • To develop and present autoSNPdb, an integrated database of SNPs and gene annotations for barley.
  • To provide a user-friendly platform for exploring genetic polymorphism data.
  • To facilitate the use of SNPs for genetic studies in barley and other species.

Main Methods:

  • Extension of the autoSNP method to create autoSNPdb, incorporating SNP and gene annotation data.
  • Development of a graphical viewer for data exploration.
  • Application of the software to public barley expressed sequence data.
  • Calculation of confidence scores based on sequence redundancy and haplotype co-segregation.

Main Results:

  • Identification of an average of one SNP per 240 bp in barley expressed sequences.
  • SNPs were found to be more prevalent in 5' regions and simple sequence repeat (SSR) flanking sequences.
  • autoSNPdb allows searching and viewing SNPs by sequence, functional annotation, or synteny with the rice genome.
  • Correlation data between SNPs and barley cultivar, tissue type, and developmental stage were collated.

Conclusions:

  • autoSNPdb offers a valuable resource for genetic polymorphism information across various species with available sequence data.
  • The database aids in understanding genotype-phenotype relationships and genetic diversity.
  • The integrated approach enhances the reliability and utility of identified SNPs for research.