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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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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%...
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Genome-wide Association Studies-GWAS01:11

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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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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...
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Rice SNP-seek database update: new SNPs, indels, and queries.

Locedie Mansueto1, Roven Rommel Fuentes1, Frances Nikki Borja1

  • 1International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.

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The updated Rice SNP-Seek Database offers enhanced querying of single nucleotide polymorphism (SNP) datasets across multiple rice genomes. This resource facilitates streamlined gene-trait association discovery for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • The Rice SNP-Seek Database provides a valuable resource for exploring genetic variation in rice.
  • Previous versions required updates to accommodate new data and improve user accessibility.

Purpose of the Study:

  • To describe significant updates and new features implemented in the Rice SNP-Seek Database.
  • To enhance data accessibility, querying capabilities, and analytical functions for rice genetic research.

Main Methods:

  • A new SNP-calling pipeline and filtering process were employed to generate comprehensive SNP datasets.
  • The pipeline was applied to multiple rice genome assemblies, including Nipponbare, IR 64, 93-11, DJ 123, and Kasalath.
  • JBrowse was integrated for visualization of various annotation tracks and genome comparison, alongside middleware redesign for performance optimization.

Main Results:

  • Complete, base, filtered, and core SNP datasets were generated for multiple rice varieties.
  • New genotype query and display features, along with an integrated list manager and SNP Annotator, were implemented.
  • Web-service access was established for most data, enabling seamless querying across biological entities.

Conclusions:

  • The updated Rice SNP-Seek Database offers significantly improved functionality for querying and analyzing rice genetic data.
  • These enhancements represent a significant step towards semi-automated gene-trait association discovery in rice.