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IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

Emanuel Maldonado1, Kartik Sunagar2, Daniela Almeida2

  • 1CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.

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|October 21, 2014
PubMed
Summary

Identifying genes under natural selection is key to understanding adaptive evolution. IMPACT_S software integrates multiple analysis tools to streamline the detection of protein evolution sites, aiding evolutionary biology research.

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Understanding adaptive evolution requires identifying genes affected by natural selection.
  • Manual analysis of selection regimes on protein-coding genes is time-consuming.
  • Non-synonymous mutations can significantly alter protein structure and function.

Purpose of the Study:

  • To develop an integrated software tool for analyzing evolutionary selection on protein-coding genes.
  • To simplify the process of identifying sites under positive, negative, or neutral selection.
  • To facilitate the visualization of selected sites on protein 3D structures.

Main Methods:

  • Developed IMPACT_S, a Graphical User Interface (GUI) software.
  • Integrated results from Codeml, Datamonkey, and TreeSAAP.
  • Incorporated tools for 3D protein structure mapping and phylogenetic analysis.

Main Results:

  • IMPACT_S effectively integrates, filters, and combines selection analysis results.
  • The software identifies and tabulates sites under different selection pressures.
  • Demonstrated functionality with a case study on reptilian Cysteine-rich Secretory Proteins (CRiSPs).

Conclusions:

  • IMPACT_S offers a rapid and effective solution for analyzing selection on protein-coding genes.
  • The software aids in understanding adaptive evolution by identifying key genetic sites.
  • IMPACT_S is a valuable, freely available tool for evolutionary biologists.