Three computational tools for predicting bacterial essential genes.
Three computational tools for predicting bacterial essential genes.
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DOI：
10.1007/978-1-4939-2398-4_13
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发表时间：
2015-01-01
期刊：
影响因子：
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通讯作者：
Wei, Wen
中科院分区：
文献类型：
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作者：
Guo, Feng-Biao;Ye, Yuan-Nong;Wei, Wen
必需基因是那些对任何活细胞的生存不可或缺的基因。细菌必需基因构成合成生物学的基石，并且通常是开发抗生素和疫苗的有吸引力的靶标。由于湿实验室方法鉴定必需基因往往意味着昂贵的经济成本和巨大的劳动力，科学家们转而寻求计算预测的替代方法。为了帮助解决这个问题，我们的研究小组（CEFG：计算、比较、进化和功能基因组学小组，http://cefg.uestc.edu.cn）构建了三个在线服务来预测细菌基因组中的必需基因。这些免费提供的工具适用于没有注释功能的单基因序列、具有明确名称的单基因以及细菌菌株的完整基因组。为了确保可靠的预测，所调查的物种应分别与参考物种之一属于同一科（对于EGP）或门（对于CEG_Match和Geptop）。作为该问题的试点软件，对它们的预测精度进行了评估，并与现有的算法进行了比较，并注意到所有其他已发布的算法都没有形成任何在线服务。我们希望CEFG的这些服务将帮助科学家和研究人员在必需基因领域。
Essential genes are those genes indispensable for the survival of any living cell. Bacterial essential genes constitute the cornerstones of synthetic biology and are often attractive targets in the development of antibiotics and vaccines. Because identification of essential genes with wet-lab ways often means expensive economic costs and tremendous labor, scientists changed to seek for alternative way of computational prediction. Aiming to help to solve this issue, our research group (CEFG: group of Computational, Comparative, Evolutionary and Functional Genomics, http://cefg.uestc.edu.cn) has constructed three online services to predict essential genes in bacterial genomes. These freely available tools are applicable for single gene sequences without annotated functions, single genes with definite names, and complete genomes of bacterial strains. To ensure reliable predictions, the investigated species should belong to the same family (for EGP) or phylum (for CEG_Match and Geptop) with one of the reference species, respectively. As the pilot software for the issue, predicting accuracies of them have been assessed and compared with existing algorithms, and note that all of other published algorithms have not any formed online services. We hope these services at CEFG will help scientists and researchers in the field of essential genes.