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Related Concept Videos

Mutations01:39

Mutations

94.5K
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
While point mutations are changes in a single nucleotide in...
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Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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Viral Mutations00:36

Viral Mutations

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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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Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

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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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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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Related Experiment Video

Updated: Feb 2, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
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Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets.

Jedidiah Carlson1,2, Jun Z Li3,4, Sebastian Zöllner5,6

  • 1Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA. jedidiah@umich.edu.

BMC Genomics
|November 30, 2018
PubMed
Summary

Helmsman is a new, fast computational tool for analyzing cancer mutation signatures in large sequencing datasets. It overcomes the limitations of existing software, enabling efficient evaluation of mutational processes in massive genomic data.

Keywords:
Cancer genomicsMutational signaturesPythonSingle nucleotide variants

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Area of Science:

  • Genomics
  • Computational Biology
  • Cancer Research

Background:

  • Cancer genomes exhibit somatic single-nucleotide variants reflecting mutational processes.
  • Identifying these mutational signatures offers clinically actionable insights into cancer etiology.
  • Current software tools struggle to analyze large-scale cancer genomic datasets efficiently.

Purpose of the Study:

  • To introduce Helmsman, a novel computational program for mutation signature analysis.
  • To address the scalability limitations of existing software for large sequencing datasets.

Main Methods:

  • Development of Helmsman, a program optimized for mutation signature analysis.
  • Designed to handle arbitrarily large sequencing datasets.

Main Results:

  • Helmsman achieves up to 300x speed improvement over existing software.
  • Its memory usage is independent of variant count, enabling analysis of previously intractable datasets.
  • Successfully analyzes massive sequencing datasets exceeding memory limitations of other programs.

Conclusions:

  • Helmsman provides a computationally efficient solution for evaluating mutational signatures in massive datasets.
  • This tool makes large-scale genomic data analysis for cancer research more accessible.
  • Helmsman is freely available for public use.