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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%...
Key Elements for Plant Nutrition02:35

Key Elements for Plant Nutrition

Like all living organisms, plants require organic and inorganic nutrients to survive, reproduce, grow and maintain homeostasis. To identify nutrients that are essential for plant functioning, researchers have leveraged a technique called hydroponics. In hydroponic culture systems, plants are grown—without soil—in water-based solutions containing nutrients. At least 17 nutrients have been identified as essential elements required by plants. Plants acquire these elements from the atmosphere, the...

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants.

Chris Duran1, Nikki Appleby, Terry Clark

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

Nucleic Acids Research
|October 16, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a cost-effective pipeline for discovering single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) data. The developed database provides a user-friendly platform for accessing and analyzing these valuable genetic markers in crops.

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Area of Science:

  • Genomics and Bioinformatics
  • Plant Genetics and Breeding

Background:

  • Single nucleotide polymorphisms (SNPs) are crucial genetic markers due to their abundance and low mutation rates.
  • Identifying SNPs associated with functional genes is essential for genetic studies and crop improvement.
  • Expressed Sequence Tag (EST) data offers a cost-effective resource for SNP discovery.

Purpose of the Study:

  • To develop an integrated pipeline for discovering single nucleotide polymorphisms (SNPs) from assembled EST sequences.
  • To create a centralized, relational database for storing and managing SNP data along with associated annotation information.
  • To provide researchers with efficient tools for identifying and analyzing SNPs in important crop species.

Main Methods:

  • Development of an integrated SNP discovery pipeline utilizing assembled EST sequences.
  • Creation of a custom relational database to store SNP data, EST source, and annotation details.
  • Implementation of search functionalities including BLAST, keyword searches, Gene Ontology (GO) annotations, and syntenic region comparisons.

Main Results:

  • Successfully identified large numbers of SNPs associated with functional genes from EST data.
  • The database currently hosts SNP data for rice, barley, and Brassica.
  • Users can efficiently query and visualize polymorphic sequences and perform targeted mapping and association studies.

Conclusions:

  • The developed SNP discovery pipeline and database provide a valuable, cost-effective resource for plant genomics research.
  • The integrated system facilitates rapid identification and analysis of SNPs, supporting genetic mapping and breeding efforts.
  • The freely accessible database promotes wider adoption and utilization of SNP data in crop science.