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Updated: May 22, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.

Trevor Paterson1, Martin Graham, Jessie Kennedy

  • 1The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Scotland, UK. trevor.paterson@roslin.ed.ac.uk

BMC Bioinformatics
|May 22, 2012
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Summary

VIPER (Visual Pedigree Explorer) effectively identifies and visualizes errors in genetic pedigree data. This tool aids researchers in cleaning complex datasets for accurate genetic inheritance analysis.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Pedigree genotype datasets are crucial for genetic inheritance analysis and marker trait mapping.
  • These datasets often contain errors in pedigree structure and individual genotypes, leading to invalid analyses.
  • Expert exploration of inconsistencies within the pedigree context is necessary for data cleaning.

Purpose of the Study:

  • To develop and evaluate VIPER (Visual Pedigree Explorer), a software tool for identifying and visualizing errors in pedigree genotype datasets.
  • To provide a user-friendly interface for domain experts to explore inheritance inconsistencies.
  • To facilitate the cleaning of complex genetic datasets.

Main Methods:

  • Development of VIPER, integrating an inheritance-checking algorithm with space-efficient pedigree visualization.
  • Overlaying reported inheritance inconsistencies onto an interactive, navigable pedigree representation.
  • Evaluation of VIPER's display and functionality with real and simulated pedigree genotype datasets, involving domain experts (geneticists).

Main Results:

  • VIPER effectively displays various scales and types of experimental datasets.
  • The interface successfully exposes and allows exploration of different error types in pedigree genotype data.
  • User evaluations confirmed the utility and usability of the VIPER interface for domain experts.

Conclusions:

  • The VIPER display effectively exposes errors in genotyped pedigrees, enabling users to investigate inheritance inconsistencies.
  • VIPER serves as a foundation for a comprehensive data cleaning tool.
  • The tool will allow users to remove erroneous data points and test the impact of data exclusions.