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WorfDB: the Caenorhabditis elegans ORFeome Database
Philippe Vaglio1, Philippe Lamesch, Jérôme Reboul
1Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Smith 858, 1 Jimmy Fund Way, Boston, MA 02115, USA. philippe_vaglio@dfci.harvard.edu
Nucleic Acids Research
|January 10, 2003
Summary
WorfDB provides a searchable database of Caenorhabditis elegans Open Reading Frames (ORFs), aiding researchers by verifying clone quality and correcting gene structures. This resource supports the broader scientific community and future ORFeome projects.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- The Caenorhabditis elegans genome sequencing consortium predicted approximately 19,000 protein-encoding Open Reading Frames (ORFs).
- Accurate annotation and experimental validation of these ORFs are crucial for understanding worm biology.
Purpose of the Study:
- To create a centralized database, WorfDB (Worm ORFeome DataBase), for the Caenorhabditis elegans ORFeome.
- To provide the scientific community with a resource to search for the availability and quality of cloned ORFs.
- To disseminate data from the cloning of the complete set of predicted ORFs.
Main Methods:
- Integration and curation of data from the cloning of approximately 19,000 predicted Caenorhabditis elegans ORFs.
- Generation of ORF sequence tags (OSTs) for individual clones.
- Development of a searchable web-based database (WorfDB).
Main Results:
- WorfDB now serves as a central repository for ORFeome data.
- ORF sequence tags (OSTs) have enabled exon structure corrections for approximately 3,400 ORFs.
- OSTs have been generated for approximately 4,300 predicted genes lacking ESTs, improving gene annotation.
Conclusions:
- WorfDB facilitates access to validated Caenorhabditis elegans ORFs, supporting functional genomics research.
- The database has already contributed to refining the annotation of the C. elegans genome.
- WorfDB serves as a model for establishing similar databases for other metazoan ORFeome projects.