A drosophila full-length cDNA resource
Background: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages. Results: We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40 percent of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing. Conclusions: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Laboratory Directed Research and Development; National Institutes of Health (US)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 813525
- Report Number(s):
- LBNL-52636; R&D Project: 80ADLE; TRN: US200316%%249
- Journal Information:
- Genome Biology, Vol. 3, Issue 12; Other Information: Journal Publication Date: December 2002; PBD: 9 May 2003
- Country of Publication:
- United States
- Language:
- English
Similar Records
The Drosophila gene collection: Identification of putative full-length cDNAs for 70 percent of D. melanogaster genes
Rapid and Efficient cDNA Library Screening by Self-Ligation ofInverse PCR Products (SLIP)