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Gramene, a tool for grass genomics.

Doreen H Ware1, Pankaj Jaiswal, Junjian Ni

  • 1Cold Spring Harbor Laboratory, New York 11724, USA.

Plant Physiology
|December 14, 2002
PubMed
Summary
This summary is machine-generated.

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Gramene is a comprehensive database for grass genomes, offering comparative mapping and curated data for rice (Oryza sativa). It integrates genetic, physical, and sequence maps to facilitate cross-species research in cereals.

Area of Science:

  • Plant genomics
  • Bioinformatics
  • Comparative genomics

Background:

  • Gramene serves as a vital community resource for rice (Oryza sativa) and other grasses.
  • It integrates diverse data types including genomic sequences, genetic maps, and curated mutant information.

Purpose of the Study:

  • To provide an overview of the search tools available in Gramene.
  • To highlight Gramene's role in comparative genome analysis across grass species.
  • To showcase the integration of curated and semi-automatically generated data.

Main Methods:

  • Development of a semi-automatically generated database for cereal sequences and genetic maps.
  • Curated extraction of detailed information from published sources for rice mutants, markers, and proteins.

Related Experiment Videos

  • Utilizing controlled vocabularies (Gene Ontology, Plant Ontology, Trait Ontology) for annotation and cross-species comparisons.

    • Main Results:

    • Gramene provides integrated genetic, physical, and sequence-based maps for rice.
    • Comparative maps are established for multiple grass species (rice, maize, sorghum, barley, wheat, oat) anchored by curated correspondences.
    • Proteins and genetic variants are annotated using standardized ontologies for functional and phenotypic descriptions.

    Conclusions:

    • Gramene offers powerful search tools for the plant research community.
    • The database facilitates comparative genomics and cross-species analysis within the grass family.
    • Standardized annotations enhance data discoverability and enable robust comparisons across diverse plant groups.