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Related Concept Videos

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.
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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate

Zena Lapp1, Hyejin Yoon1, Brian Foley1

  • 1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Biorxiv : the Preprint Server for Biology
|November 18, 2024
PubMed
Summary
This summary is machine-generated.

The updated Hypermut software identifies virus sequences with APOBEC3-induced mutations. This tool improves sequence analysis by excluding non-representative hypermutated sequences and handling complex alignments.

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Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • APOBEC3F and APOBEC3G enzymes induce G to A hypermutation in viral sequences.
  • Hypermutated sequences can skew viral evolution studies and downstream analyses.
  • Previous Hypermut versions lacked support for multistate characters and gaps.

Purpose of the Study:

  • To present an enhanced, user-friendly Hypermut tool for detecting viral hypermutation.
  • To incorporate functionality for handling multistate characters and gaps in sequence alignments.
  • To facilitate seamless integration of hypermutation detection into sequence analysis pipelines.

Main Methods:

  • Development of a new version of the Hypermut software.
  • Implementation of a user-friendly web and command-line interface.
  • Inclusion of algorithms to process multistate characters and gaps in sequence data.

Main Results:

  • The updated Hypermut tool effectively detects hypermutation events, including G to A mutations.
  • The software now accommodates multistate characters and gaps, enhancing its applicability.
  • The tool provides straightforward integration into existing sequence analysis workflows.

Conclusions:

  • The enhanced Hypermut tool offers improved accuracy and versatility for identifying hypermutated viral sequences.
  • This advancement aids in obtaining more representative results in viral evolution and sequence analysis.
  • The tool supports the specification of any mutational pattern and context beyond G to A events.