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Related Concept Videos

Mutations01:39

Mutations

Overview
Mutations01:39

Mutations

Overview
Mutations01:35

Mutations

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
While point mutations are changes in a single nucleotide in...
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

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...
Mutations in Microorganisms01:18

Mutations in Microorganisms

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,...
Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

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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Related Experiment Video

Updated: May 9, 2026

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing
11:36

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

Plot protein: visualization of mutations.

Tychele Turner1

  • 1Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N, Broadway, MRB 572, Baltimore, MD 21205, USA. tturne18@jhmi.edu.

Journal of Clinical Bioinformatics
|July 24, 2013
PubMed
Summary
This summary is machine-generated.

Plot Protein is a free tool that visualizes amino acid changes in proteins, aiding disease mechanism discovery. This method helps researchers quickly understand mutation patterns from sequencing data.

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Last Updated: May 9, 2026

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) allows DNA variation analysis.
  • Evaluating variants at the protein level provides deeper biological insights.
  • Visualizing protein variation reveals patterns not evident in text data.

Purpose of the Study:

  • To introduce Plot Protein, a tool for visualizing amino acid changes.
  • To enable researchers to plot protein variation from sequencing studies uniformly.
  • To demonstrate how protein variation visualization aids in understanding disease mechanisms.

Main Methods:

  • Developed Plot Protein, a freely available tool.
  • The tool is accessible via command line or a web browser graphical interface.
  • Features include plotting amino acid changes, domains, post-translational modifications, and conservation.

Main Results:

  • Plot Protein enables quick and uniform visualization of protein variation.
  • The tool was used to analyze the RET protein in Multiple Endocrine Neoplasia 2A (MEN2A).
  • Clustering of mutations within the RET protein provided insights into MEN2A disease mechanisms.

Conclusions:

  • Plot Protein is a valuable tool for studying amino acid changes and their protein localization.
  • Both command-line and web server versions are available for users.
  • The software facilitates deriving visual knowledge about protein mutations.