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Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics
Yuichi Ito1, Kohji Arikawa, Baltazar A Antonio
1Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan. yuito@staff.or.jp
Nucleic Acids Research
|December 21, 2004
Summary
A new Rice Annotation Database aids rice genomics research by integrating manual gene annotations and providing visualization, query, and analysis tools. This resource facilitates comparative genomics and structural analysis of the rice genome.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Map-based rice genomics requires integrated genome annotation.
- Existing resources may lack comprehensive manual curation and comparative analysis features.
Purpose of the Study:
- To construct a contig-oriented database for rice genome annotation.
- To facilitate map-based rice genomics and comparative analysis.
Main Methods:
- Developed a database integrating manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones.
- Implemented features for concise visualization, user-friendly querying, data download, genome feature analysis, and genome-wide homology searches (BLAST).
Main Results:
- The Rice Annotation Database contains 215 Mb of sequence with 30,000 manually curated genes (as of October 2004).
- Provides visualization of predicted genes, prediction program results, and homology data (EST, cDNA, protein).
- Enables analysis of genome features (e.g., GC-content) and comparative genomics.
Conclusions:
- The database offers the latest manual annotation information and comprehensive structural analysis of the rice genome.
- Facilitates advanced rice genomics research through integrated data and analysis tools.
- Accessible at http://rad.dna.affrc.go.jp/