ArticleProceedings of the National Academy of Sciences of the United States of America2005
A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models.BMC genomics · 2019Article
- De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.PLoS genetics · 2013Article
- A beginner's guide to eukaryotic genome annotation.Nature reviews. Genetics · 2012Review
- De novo origins of human genes.PLoS genetics · 2011Article
- Quantitative measures for the management and comparison of annotated genomes.BMC bioinformatics · 2009Article
- MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.Genome research · 2008Article
- Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.Genome research · 2007Article
- Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.Nature · 2007Article
- Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury.BMC genomics · 2007Article
- A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila.Genome biology · 2007Article
- Applications of high-throughput RNA interference screens to problems in cell and developmental biology.Genetics · 2007Review
- Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.Genome biology · 2006Article
- Selective constraint on noncoding regions of hominid genomes.PLoS computational biology · 2005Article
- Molecular population genetics of accessory gland protein genes and testis-expressed genes in Drosophila mojavensis and D. arizonae.Genetics · 2005Article
- Begin at the beginning: predicting genes with 5' UTRs.Genome research · 2005Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Five years after the completion of the sequence of the Drosophila melanogaster genome, the number of protein-coding genes it contains remains a matter of debate; the number of computational gene predictions greatly exceeds the number of validated gene annotations. We have assembled a collection of >10,000 gene predictions that do not overlap existing gene annotations and have developed a process for their validation that allows us to efficiently prioritize and experimentally validate predictions from various sources by sequencing RT-PCR products to confirm gene structures. Our data provide experimental evidence for 122 protein-coding genes. Our analyses suggest that the entire collection of predictions contains only approximately 700 additional protein-coding genes. Although we cannot rule out the discovery of genes with unusual features that make them refractory to existing methods, our results suggest that the D. melanogaster genome contains approximately 14,000 protein-coding genes.
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