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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of

Alsamman M Alsamman1, Achraf El Allali2, Morad M Mokhtar1,2

  • 1Agricultural Genetic Engineering Research Institute, Giza, Egypt.

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|September 20, 2023
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Summary

AlignStatPlot simplifies complex multiple sequence alignment (MSA) post-analysis for researchers. This R package and online tool offers robust data visualization and analysis for genetic variations.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genetics

Background:

  • Multiple sequence alignment (MSA) is crucial for identifying genetic variations linked to phenotypic traits.
  • Post-analysis of MSA data is challenging for non-programmers, especially with large datasets and complex variations like indels.
  • Existing tools lack integrated post-MSA analysis combining sequence data, gene annotations, and cluster analysis.

Purpose of the Study:

  • To introduce AlignStatPlot, an R package and online tool designed for accessible post-MSA analysis.
  • To provide researchers with a user-friendly solution for analyzing and visualizing genetic diversity data.
  • To facilitate the integration of gene-level and single nucleotide-level data with annotations for advanced analysis.

Main Methods:

  • Development of an R package and a web-based tool named AlignStatPlot.
  • Implementation of both traditional and advanced analytical methods for sequencing data.
  • Creation of novel visualization techniques for MSA results, including single-page views.

Main Results:

  • AlignStatPlot offers robust handling and visualization of genetic diversity data.
  • The tool enables post-MSA analysis combining sequence variations, gene annotations, and cluster analysis.
  • The online version streamlines analysis, saving researchers time and allowing focus on interpretation.

Conclusions:

  • AlignStatPlot addresses the need for user-friendly post-MSA analysis tools in population genetics.
  • The package and online tool enhance the ability to study genetic variations and population diversity.
  • AlignStatPlot is a valuable, easy-to-use supplement to existing population genetics software.