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Related Experiment Videos

The Rice Annotation Project Database (RAP-DB): 2008 update.

1, Tsuyoshi Tanaka, Baltazar A Antonio

  • 1National Institute of Agrobiological Sciences, Ibaraki 305-8602, Japan.

Nucleic Acids Research
|December 20, 2007
PubMed

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Summary
This summary is machine-generated.

The updated Rice Annotation Project Database (RAP-DB) offers manually curated genome annotation for rice biology. This resource provides comprehensive genomics data, including gene functions and sequences, aiding researchers in understanding rice genetics.

Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Biology

Background:

  • The International Rice Genome Sequencing Project (IRGSP) has undergone revisions and reassembly.
  • Numerous rice-expressed sequence tags and functional genomics resources have become available globally.
  • Previous versions of RAP-DB require updating to reflect new genomic information.

Purpose of the Study:

  • To provide an updated and manually curated genome annotation for rice.
  • To integrate new genomic data and resources into the Rice Annotation Project Database (RAP-DB).
  • To enhance user access to comprehensive rice biology information.

Main Methods:

  • Manual curation of functional descriptions for all rice genes.
  • Incorporation of revised and reassembled IRGSP genome assembly.

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  • Integration of data from massively parallel signature sequencing (MPSS) technology and sequence similarity.

    • Main Results:

    • The latest RAP-DB version includes detailed annotation for 31,439 genes validated by cDNAs.
    • Annotation data encompasses clone positions, gene structures, functions, RNA genes, and flanking sequences of mutant lines.
    • New keyword search system developed for improved user data access.

    Conclusions:

    • The updated RAP-DB serves as a vital resource for rice genomics research.
    • Enhanced annotation facilitates a comprehensive understanding of rice biology.
    • The database provides valuable comparative genomics data with other annotation sources like Gnomon.