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HOPPSIGEN: a database of human and mouse processed pseudogenes.

Adel Khelifi1, Khelifi Adel, Laurent Duret

  • 1Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard-Lyon 1, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. khelifi@biomserv.univ-lyon1.fr

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

Processed pseudogenes, non-functional gene copies, are valuable neutral markers for genome evolution studies. A new method accurately annotates these sequences, creating a high-quality database for research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Evolution

Background:

  • Processed pseudogenes arise from retrotransposition of mRNA and lack functional promoters.
  • They accumulate mutations freely, making their ancestral structure inferable from functional homologs.
  • These characteristics position processed pseudogenes as ideal neutral markers for genome evolution analysis.

Purpose of the Study:

  • To develop and implement a robust method for annotating processed pseudogenes in complete genomes.
  • To create a high-quality, curated dataset of processed pseudogenes for research applications.
  • To facilitate the use of processed pseudogenes in gene prediction, functional genomics, and evolutionary studies.

Main Methods:

  • Screening of human and mouse genomes (ENSEMBL) for processed pseudogenes derived from intron-containing genes.

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  • Employment of a conservative detection strategy to minimize false positive identifications.
  • Classification of retroelements, strictly defining processed pseudogenes based on conserved open reading frames and gene location overlaps.

    • Main Results:

    • Annotation of 5823 retroelements (5206 processed pseudogenes) in the human genome.
    • Annotation of 3934 retroelements (3428 processed pseudogenes) in the mouse genome.
    • Generation of a high-quality dataset, potentially underestimating total counts but ensuring reliability.

    Conclusions:

    • The developed method provides a reliable approach for identifying and annotating processed pseudogenes.
    • The curated dataset and the HOPPSIGEN database offer valuable resources for studying genome structure and evolution.
    • Processed pseudogenes serve as crucial markers for understanding evolutionary dynamics and improving genome annotation.