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COVTree: Coevolution in OVerlapped sequences by Tree analysis server.

Elin Teppa1, Diego J Zea1, Francesco Oteri1

  • 1Sorbonne Université, UPMC Univ Paris 06, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France.

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This summary is machine-generated.

Molecular coevolution in overlapping viral genes helps proteins tolerate mutations. The COVTree web server analyzes these coevolving amino acid pairs to understand their functional impacts.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Overlapping genes are common in viruses and crucial for their function and evolution.
  • Molecular coevolution can mitigate evolutionary constraints in overlapping regions, allowing for mutation tolerance and compensation.
  • Understanding coevolutionary patterns in these regions offers insights into mutation effects on proteins.

Purpose of the Study:

  • To introduce COVTree (Coevolution in OVerlapped sequences by Tree analysis), a web server for analyzing coevolving amino acid pairs in overlapping genes.
  • To provide a tool that can handle diverse protein families, including those with conserved sequences.
  • To facilitate the biological interpretation of coevolutionary signatures.

Main Methods:

  • COVTree utilizes BIS2, an accelerated version of the Blocks in Sequences (BIS) coevolution analysis tool.
  • The server analyzes coevolving amino acid pairs, considering residues both inside and outside the overlapping gene regions.
  • It incorporates an interactive graphical interface for result interpretation.

Main Results:

  • COVTree enables online analysis of coevolving amino acid pairs within overlapping viral genes.
  • The tool is designed to accommodate protein families with varying characteristics, including low sequence diversity.
  • It offers a user-friendly interface for exploring coevolutionary data.

Conclusions:

  • COVTree provides a valuable resource for studying molecular coevolution in overlapping genes.
  • The analysis of coevolving residues can reveal functional relationships and evolutionary mechanisms.
  • The web server enhances the accessibility and interpretability of coevolutionary analyses for researchers.