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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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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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Spontaneous and Induced Mutations01:30

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Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Mutations01:39

Mutations

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Overview
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Mutations01:35

Mutations

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Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
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CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure.

Zhenpeng Li1, Yang Huang1, Yabo Ouyang1

  • 1State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.

Bioinformatics (Oxford, England)
|April 1, 2014
PubMed
Summary

Correlated mutations are key to understanding evolution. The CorMut R package helps analyze these genetic changes at the codon or amino acid level, visualizing them as networks.

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Area of Science:

  • Evolutionary Biology
  • Genetics
  • Bioinformatics

Background:

  • Correlated mutations are crucial for understanding the genetic mechanisms driving evolution.
  • Analyzing these mutations provides insights into evolutionary processes.
  • Identifying patterns in correlated mutations can reveal functional constraints and adaptive pathways.

Purpose of the Study:

  • To introduce CorMut, an R package for computing and analyzing correlated mutations.
  • To provide a tool for investigating evolutionary genetic mechanisms at the codon or amino acid level.
  • To facilitate the comparison of correlated mutation patterns under different evolutionary conditions.

Main Methods:

  • CorMut implements three classical methods for detecting correlated mutations.
  • The package computes correlations at the unit of codon or amino acid mutation.
  • Results are visualized as correlation mutation networks.

Main Results:

  • CorMut successfully computes correlated mutations, offering insights into evolutionary relationships.
  • The package enables the visualization of mutation correlations as networks.
  • Comparative analysis of correlated mutations across different evolutionary scenarios is supported.

Conclusions:

  • CorMut is a valuable R package for evolutionary biologists and geneticists.
  • The tool aids in understanding the genetic basis of evolution through correlated mutation analysis.
  • CorMut facilitates the exploration of evolutionary dynamics by comparing mutation patterns.