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Related Experiment Videos

GeneTrees: a phylogenomics resource for prokaryotes.

Yuying Tian1, Allan W Dickerman

  • 1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA.

Nucleic Acids Research
|December 8, 2006
PubMed
Summary
This summary is machine-generated.

The GeneTrees system offers a comprehensive database of gene phylogenies for 325 prokaryote genomes, aiding evolutionary analysis. It provides tools for exploring evolutionary models of protein-coding genes across diverse species.

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Area of Science:

  • Comparative genomics
  • Phylogenetics
  • Bioinformatics

Background:

  • Comparative genomics relies on analyzing gene families and their evolutionary histories.
  • Understanding gene evolution is crucial for deciphering genome function and organization.
  • Previous methods lacked comprehensive, integrated resources for large-scale gene family analysis.

Purpose of the Study:

  • To develop and present the GeneTrees phylogenomics system.
  • To provide detailed evolutionary models for protein-coding genes in fully sequenced genomes.
  • To create a publicly accessible database for exploring gene phylogenies.

Main Methods:

  • Utilizing a homology group discovery tool for identifying related protein sets.
  • Performing multiple sequence alignments and phylogenetic tree inference for each group.
  • Developing a graphical web interface for database exploration and visualization.

Main Results:

  • A database containing alignments and phylogenetic trees for 890,000 protein sequences from 325 prokaryote genomes.
  • Over 100,000 homology groups, each with an associated phylogenetic tree.
  • A web interface enabling querying by sequence identifiers or annotation terms and visual browsing of genomes.

Conclusions:

  • The GeneTrees system provides a valuable resource for comparative genomic and phylogenomic studies.
  • The database facilitates the detailed evolutionary analysis of protein-coding genes.
  • The graphical interface enhances the accessibility and utility of phylogenomic data for researchers.