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Xpro: database of eukaryotic protein-encoding genes.

Vivek Gopalan1, Tin Wee Tan, Bernett T K Lee

  • 1Department of Biochemistry, National University of Singapore, Singapore 119260.

Nucleic Acids Research
|December 19, 2003
PubMed
Summary

Xpro is a comprehensive eukaryotic gene database, integrating GenBank data with detailed annotations on introns, exons, and splice sites. It validates gene structures and identifies alternative splicing events for enhanced genomic analysis.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Eukaryotic gene architecture analysis requires comprehensive sequence data and annotations.
  • Existing databases may lack detailed information on splice sites, intron phases, and alternative splicing.

Purpose of the Study:

  • To develop Xpro, a relational database for eukaryotic protein-encoding DNA sequences.
  • To provide detailed annotations and validation of eukaryotic gene architecture, including introns and exons.
  • To facilitate the study of alternative splicing and gene classification.

Main Methods:

  • Integrated GenBank records with associated data on gene architecture.
  • Annotated splice sites and intron phases.
  • Validated intron positions using sequence alignment with dbEST.
  • Cross-referenced with Swiss-Prot/TrEMBL and Pfam for non-redundancy.

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  • Classified genes as experimental or predicted.

    • Main Results:

    • Xpro contains 493,983 genes (351,918 intron-containing, 142,065 intron-less).
    • Provides validated intron positions and alternative splicing information.
    • Offers an Entrez-like query system for data access.
    • Includes annotations on splice sites and intron phases.

    Conclusions:

    • Xpro serves as a valuable resource for eukaryotic gene architecture analysis.
    • The database facilitates the identification and study of alternative splicing.
    • Xpro offers a validated and comprehensive collection of eukaryotic gene information.