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PROBE: analysis and visualization of protein block-level evolution.

Arnaud Kress1, Odile Lecompte1, Olivier Poch1

  • 1Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France.

Bioinformatics (Oxford, England)
|May 10, 2018
PubMed
Summary
This summary is machine-generated.

PROBE is a new tool for identifying conserved protein regions, or blocks, within multiple sequence alignments. This helps in understanding protein evolution and function.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary biology

Background:

  • Comparative genomics relies on analyzing protein sequence conservation.
  • Identifying conserved regions ab initio in protein multiple alignments is challenging.
  • Existing tools lack efficiency for automatic conservation analysis.

Purpose of the Study:

  • To introduce PROBE, an automated tool for identifying conserved regions in protein multiple alignments.
  • To detect conserved blocks at both family and sub-family levels.
  • To facilitate studies on sequence-structure-function-evolution relationships.

Main Methods:

  • PROBE performs fully automatic analysis of protein family conservation.
  • Identifies conserved regions ('blocks') corresponding to structural/functional domains or motifs.
  • Maps conserved blocks onto phylogenetic trees and visualizes them within multiple sequence alignments.

Main Results:

  • PROBE identifies family-level blocks crucial for protein structure/function.
  • Sub-family level blocks highlight functional specialization (e.g., binding partners).
  • Visualizations aid in in-depth analysis of evolutionary relationships.

Conclusions:

  • PROBE offers an efficient, automated solution for identifying conserved protein regions.
  • The tool supports detailed studies of protein evolution and function.
  • Enables block-level phylogenetic profiling for deeper biological insights.