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% 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.
Stapleton
Mark
M
Berkeley Drosophila Genome Project Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. staple@fruitfly.org
Carlson
Joe
J
Brokstein
Peter
P
Yu
Charles
C
Champe
Mark
M
George
Reed
R
Guarin
Hannibal
H
Kronmiller
Brent
B
Pacleb
Joanne
J
Park
Soo
S
Wan
Ken
K
Rubin
Gerald M
GM
Celniker
Susan E
SE
D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000032:analysis*; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000737:chemistry / Q000235:genetics*; D017344:Genes, Insect; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods
D018076:DNA, Complementary