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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.
FlyBase ID
FBrf0155827
Publication Type
Research paper
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.

PubMed ID
PubMed Central ID
PMC151185 (PMC) (EuropePMC)
Related Publication(s)
Personal communication to FlyBase

LysE or LysC.
Misra, 2004.1.7, LysE or LysC. [FBrf0173251]

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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Genome Biol.
    Title
    Genome Biology
    Publication Year
    2000-
    ISBN/ISSN
    1474-7596 1474-760X
    Data From Reference