Department of Physics, Tianjin University, Tianjin 300072, China.
Sci Rep. 2011;1:53. doi: 10.1038/srep00053. Epub 2011 Aug 3.
Mycoplasma, which was used to create the first "synthetic life", has been an important species in the emerging field, synthetic biology. However, essential genes, an important concept of synthetic biology, for both M. mycoides and M. capricolum, as well as 14 other Mycoplasma with available genomes, are still unknown. We have developed a gene essentiality prediction algorithm that incorporates information of biased gene strand distribution, homologous search and codon adaptation index. The algorithm, which achieved an accuracy of 80.8% and 78.9% in self-consistence and cross-validation tests, respectively, predicted 5880 essential genes in the 16 Mycoplasma genomes. The intersection set of essential genes in available Mycoplasma genomes consists of 153 core essential genes. The predicted essential genes (available from pDEG, tubic.tju.edu.cn/pdeg) and the proposed algorithm can be helpful for studying minimal Mycoplasma genomes as well as essential genes in other genomes.
支原体曾被用于创建第一个“合成生命”，它一直是新兴领域合成生物学的重要物种。然而，对于 M. mycoides 和 M. capricolum 以及其他 14 种具有可用基因组的支原体来说，其必需基因（合成生物学的一个重要概念）仍然未知。我们开发了一种基因必需性预测算法，该算法整合了基因链偏向分布、同源搜索和密码子适应指数的信息。该算法在自我一致性和交叉验证测试中的准确率分别达到了 80.8%和 78.9%，预测了 16 种支原体基因组中的 5880 个必需基因。在现有的支原体基因组中，必需基因的交集集包含 153 个核心必需基因。预测的必需基因（可从 pDEG 获得，tubic.tju.edu.cn/pdeg）和提出的算法可有助于研究最小支原体基因组以及其他基因组中的必需基因。
