Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
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DOI：
10.1186/gb-2002-3-12-research0083
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发表时间：
2002
期刊：
影响因子：
12.3
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中科院分区：
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果蝇Melanogaster基因组序列的最近完成，以及一组大大扩展的果蝇cDNA序列的可用性，为Flybase提供了显着改善基因组注释的机会。
果蝇Melanogaster基因组序列最近完成了高质量的基因组序列，以及一组大大扩展的果蝇cDNA序列的可用性，将预测的构想基因的78％保持一致，为FlyBase提供了显着改善基因组注释的机会。我们通过视觉检查每个基因，利用一套综合策划规则，需要为每个基因模型进行可追溯的证据，并将每个预测的肽与瑞士 - 普罗特和Trembl序列进行比较，从而使注释过程更加严格。
尽管果蝇中预测的蛋白质编码基因的数量基本上保持不变，但修订后的注释显着改善了基因模型，从而导致结构变化为85％的转录本和45％的预测蛋白质。我们注释可转座元件和非蛋白质编码RNA作为新特征，并扩展了未翻译（UTR）序列和替代转录本的注释，分别包括超过70％和20％的基因。最后，cDNA序列提供了dicistronic转录本，在相同的DNA序列链上重叠UTR的邻近基因，替代地编码不同的，非重叠的肽和许多嵌套基因的剪接基因。
鉴定如此多的不寻常基因模型不仅表明基因调节的某些机制比以前认为的更为普遍，而且强调了真核基因预测的复杂挑战。目前，实验数据和人类策划对于产生高质量的基因组注释仍然至关重要。
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations. 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.