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Related Experiment Videos

INE: a rice genome database with an integrated map view.

K Sakata1, B A Antonio, Y Mukai

  • 1Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.

Nucleic Acids Research
|December 11, 1999
PubMed
Summary

The Rice Genome Research Program developed INE, a new database integrating rice genomic information. This database aids researchers by correlating accumulated data with the complete rice genome sequence.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • The Rice Genome Research Program (RGP) initiated large-scale rice genome sequencing in 1998.
  • Accumulated genomic data requires integration and correlation with the genome sequence.

Purpose of the Study:

  • To develop a comprehensive database for rice genomic information.
  • To integrate and correlate existing genomic data with the rice genome sequence.

Main Methods:

  • Development of the INtegrated rice genome Explorer (INE) database.
  • Implementation of a Java applet for rapid web-based data viewing.
  • Inclusion of genetic and physical maps (YAC and PAC contigs) with graphical displays.

Main Results:

  • The first operational version of INE is complete, featuring integrated genomic data.

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  • INE includes sequences and annotations of PAC contigs, with quality control for accuracy.
  • Graphical maps facilitate understanding of marker positional relationships on chromosomes.

    • Conclusions:

    • INE serves as a central repository for rice genome sequence data.
    • The database facilitates collaboration within the International Rice Genome Sequencing Project (IRGSP).
    • INE provides a valuable resource for researchers studying the rice genome.