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Related Concept Videos

Mutations in Microorganisms01:18

Mutations in Microorganisms

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Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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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...
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Viral Mutations00:36

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Single Nucleotide Polymorphisms-SNPs01:05

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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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Evolutionary Relationships through Genome Comparisons02:54

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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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Point and Frameshift Mutations01:30

Point and Frameshift Mutations

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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Updated: Dec 14, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences.

Yue Xing1, Xiao Li2, Xiang Gao3

  • 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States.

Frontiers in Microbiology
|July 17, 2020
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Summary

Researchers can now rapidly identify SARS-CoV-2 mutations using MicroGMT, a new Python package. This tool aids in studying viral evolution and epidemiology by analyzing genomic sequences for mutations and indels.

Keywords:
COVID-19SARS-CoV-2bioinformaticsepidemiologymicrobialmolecular evolutionmutationvirus

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Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • The global spread of SARS-CoV-2 necessitates rapid identification of novel mutations.
  • Understanding viral molecular evolution and epidemiology is crucial for public health.
  • Existing tools may not be optimized for quick mutation detection in newly sequenced genomes.

Purpose of the Study:

  • To develop a user-friendly Python package for identifying genetic variations in microbial genomes.
  • To provide a tool for rapid characterization of indels and point mutations in SARS-CoV-2.
  • To offer a flexible software applicable to various microbial genomic analyses.

Main Methods:

  • Development of a Python package named MicroGMT.
  • Input processing of raw sequence reads or assembled genome sequences.
  • Comparison against reference databases to detect indels and point mutations.
  • Default optimization for SARS-CoV-2, with applicability to other microbes.

Main Results:

  • MicroGMT successfully identifies and characterizes indels and point mutations.
  • The package handles both raw and assembled genomic data.
  • The software is adaptable for analyzing genomes beyond SARS-CoV-2.

Conclusions:

  • MicroGMT provides an efficient solution for mutation detection in microbial genomics.
  • The tool supports research in viral evolution and epidemiology.
  • Freely available software facilitates broader adoption and application in scientific research.