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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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,...
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Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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.
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Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

Using mtDNA sequences to estimate SNP parameters in ESTs.

Kent M Reed1

  • 1Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA. reedx054@umn.edu

Animal Biotechnology
|July 9, 2008
PubMed
Summary
This summary is machine-generated.

Mitochondrial DNA (mtDNA) sequences in expressed sequence tag (EST) datasets can help identify valid single nucleotide polymorphisms (SNPs). This method improves SNP discovery accuracy by analyzing artifact sequences often found in large public databases.

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Published on: February 10, 2023

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08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single nucleotide polymorphism (SNP) discovery relies on extensive sequence data from public databases.
  • Existing methods like EST surveys and whole genome sequencing are prone to errors and ascertainment bias, leading to inaccurate SNP identification.
  • Mitochondrial DNA (mtDNA) sequences are often found as artifacts in cDNA libraries and are typically disregarded in SNP discovery efforts.

Purpose of the Study:

  • To investigate the utility of mitochondrial DNA (mtDNA) sequences within expressed sequence tag (EST) datasets for improving single nucleotide polymorphism (SNP) discovery.
  • To demonstrate how these artifact mtDNA sequences can be leveraged to estimate SNP parameters and predict SNP validity.

Main Methods:

  • Analysis of sequences from four turkey muscle cDNA libraries.
  • Identification and extraction of mitochondrial DNA (mtDNA) sequences from the expressed sequence tag (EST) datasets.
  • Utilizing the extracted mtDNA sequences to model and estimate single nucleotide polymorphism (SNP) parameters relevant to EST projects.

Main Results:

  • Mitochondrial DNA (mtDNA) sequences present in EST collections can serve as a valuable resource for SNP analysis.
  • These sequences allow for the estimation of key SNP parameters, aiding in the prediction of SNP validity.
  • The study demonstrates a novel approach to enhance the accuracy of SNP discovery using commonly overlooked sequence data.

Conclusions:

  • Incorporating mitochondrial DNA (mtDNA) sequence analysis into expressed sequence tag (EST) projects offers a method to improve the reliability of single nucleotide polymorphism (SNP) discovery.
  • This approach helps mitigate errors and biases inherent in large-scale sequencing efforts.
  • Leveraging artifact sequences like mtDNA can refine SNP parameter estimation and enhance the overall quality of discovered SNPs.