|Citation||Misra, S., Crosby, M.A., Mungall, C.J., Matthews, B.B., Campbell, K.S., Hradecky, P., Huang, Y., Kaminker, J.S., Millburn, G.H., Prochnik, S.E., Smith, C.D., Tupy, J.L., Whitfield, E.J., Bayraktaroglu, L., Berman, B.P., Bettencourt, B.R., Celniker, S.E., de Grey, A.D.N.J., Drysdale, R.A., Harris, N.L., Richter, J., Russo, S., Schroeder, A.J., Shu, S.Q., Stapleton, M., Yamada, C., Ashburner, M., Gelbart, W.M., Rubin, G.M., Lewis, S.E. (2002). Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 3(12): RESEARCH0083. (Export to RIS)|
|Publication Type||Research paper|
|PubMed Abstract||The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.|
|Personal communication to FlyBase||LysE or LysC.
Misra, 2004.1.7, LysE or LysC. [FBrf0173251]
What does this section display?
What does this section not display?
This section does not currently display links that were removed or gene model changes.
|All updates||Click here to see a list of all updates to this record from FB2010_08 and on.|
|Language of Publication||English|
|Additional Languages of Abstract|
|Also Published As|
|Data from Reference|