Closing in on the C elegans ORFeome by cloning TWINSCAN predictions
Closing in on the C elegans ORFeome by cloning TWINSCAN predictions
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DOI：
10.1101/gr.3329005
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发表时间：
2005-04-01
期刊：
影响因子：
7
通讯作者：
Brent, MR
中科院分区：
文献类型：
--
作者：
Wei, CC;Lamesch, P;Brent, MR
秀丽隐杆线虫的基因组是第一个被测序的动物基因组。虽然已经付出了相当大的努力来注释它，标准的WormBase注释包含数千个预测的基因，没有cDNA或EST的证据。我们假设，通过创建更准确的基因预测程序，然后扩增和测序预测的基因，可以获得更完整的实验注释。我们的方法是适应TWINSCAN基因预测系统，以线虫和C briggsae，并改善其剪接位点和内含子长度模型。由此产生的系统在精确预测开放阅读框架（ORF）方面具有60%的灵敏度和58%的特异性，因此，蛋白质是我们所知道的任何多细胞生物体的最佳结果。然后，我们试图扩增，克隆和测序265 TWINSCAN预测的ORF，不重叠WormBase基因注释。成功率为55%，将WormBase中完全缺失的146个基因添加到ORF克隆集合（ORFeome）中。同样的程序在90个Worm Base“预测”基因上有7%的成功率，这些基因不与TWINSCAN预测重叠。这些结果表明，通过用TWINSCAN预测替换其部分策划的预测基因，可以显着提高WormBase的准确性。本研究中描述的技术将继续推动线虫ORFeome的完成，并有助于目前正在测序的三种小杆线虫物种的注释。研究结果还表明，这项技术可以显着提高我们对“零件清单”的了解，即使是研究得最好的模式生物。
The genome of Caenorhabditis elegans was the first animal genome to be sequenced. Although considerable effort has been devoted to annotating it, the standard WormBase annotation contains thousands of predicted genes for which there is no cDNA or EST evidence. We hypothesized that a more complete experimental annotation could be obtained by creating a more accurate gene-prediction program and then amplifying and sequencing predicted genes. Our approach was to adapt the TWINSCAN gene prediction system to C elegans and C briggsae and to improve its splice site and intron-length models. The resulting system has 60% sensitivity and 58% specificity in exact prediction of open reading frames (ORFs), and hence, proteins-the best results we are aware of any multicellular organism. We then attempted to amplify, clone, and sequence 265 TWINSCAN-predicted ORFs that did not overlap WormBase gene annotations. The success rate was 55%, adding 146 genes that were completely absent from WormBase to the ORF clone collection (ORFeome). The same procedure had a 7% success rate on 90 Worm Base "predicted" genes that do not overlap TWINSCAN predictions. These results indicate that the accuracy of WormBase could be significantly increased by replacing its partially curated predicted genes with TWINSCAN predictions. The technology described in this study will continue to drive the C elegans ORFeome toward completion and contribute to the annotation of the three Caenorhabditis species currently being sequenced. The results also suggest that this technology can significantly improve our knowledge of the "parts list" for even the best-studied model organisms.