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A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.

Paramvir S Dehal1, Jeffrey L Boore

  • 1Evolutionary Genomics Department, DOE Joint Genome Institute and Lawrence, Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA. psdehal@lbl.gov

BMC Bioinformatics
|April 13, 2006
PubMed
Summary

The PhIGs database provides a phylogenomic resource for analyzing gene families and orthologous genes across diverse genomes. It aids in accurate functional inference and evolutionary studies by integrating gene annotations and genomic context.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Existing gene family clustering methods often fail to identify true orthologs, leading to annotation errors.
  • A phylogenetic framework is crucial for accurate gene function inference and understanding genome evolution.

Purpose of the Study:

  • To present the PhIGs database, a phylogenomic resource for sequenced genomes.
  • To provide a tool for accurate orthologous gene clustering and analysis within a phylogenetic context.

Main Methods:

  • Automated generation of evolutionary gene clusters and gene trees.
  • Determination of orthology and paralogy relationships.
  • Integration of gene annotations, expression data, and genomic context.

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Main Results:

  • The PhIGs database includes 23 genomes with 409,653 genes in 42,645 clusters, designed for orthology.
  • Gene cluster distances align with organismal relationships, enhancing ortholog likelihood.
  • Website tools enable keyword and sequence similarity searches, alongside visualization of gene positions.

Conclusions:

  • Accurate gene and genome analysis requires a full phylogenetic context.
  • The PhIGs database and website offer this essential resource for the scientific community.
  • Future expansion will include more genomes and analyses.