Prediction of genomic islands in seven human pathogens using the Z-Island method
Prediction of genomic islands in seven human pathogens using the Z-Island method
复制标题
使用 Z 岛方法预测七种人类病原体的基因组岛
DOI：
10.4238/2011.october.5.1
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发表时间：
2011-01-01
影响因子：
0.4
通讯作者：
Guo, F. -B.
中科院分区：
文献类型：
--
作者：
Wei, W.;Guo, F. -B.
我们采用了Zhang和Zhang的方法(Z-Island方法)对7种人类病原体的基因组岛进行了鉴定，并对它们的染色体DNA序列进行了分析。Z-Island方法是一种预测细菌基因组中基因组岛的理论方法；它包括确定累积GC图谱和计算密码子使用偏倚。用这种方法在7种病原菌中发现了31个基因组岛。进一步的分析表明，大多数都具有已知的保守特征；这增加了它们是真正基因组岛的可能性。11个基因组岛被发现编码与致病有关的产物(毒力因子)或与抗药性有关的产物(耐药因子)。这一发现可能有助于研究这些细菌的致病性，并有助于治疗它们引起的疾病。在对不同方法预测的基因组岛上迁移性元件分布的比较中，Z岛方法给出了较低的假阳性率。Z-Island方法被发现比我们比较的两种方法Sigi-HMM和Island Pick检测到更多的已知基因组岛。此外，它在特异性和敏感性之间保持了更好的平衡。唯一不方便的是，用Z-Island方法寻找基因组岛的步骤是半自动的。
We adopted the method of Zhang and Zhang (the Z-Island method) to identify genomic islands in seven human pathogens, analyzing their chromosomal DNA sequences. The Z-Island method is a theoretical method for predicting genomic islands in bacterial genomes; it consists of determination of the cumulative GC profile and computation of codon usage bias. Thirty-one genomic islands were found in seven pathogens using this method. Further analysis demonstrated that most have the known conserved features; this increases the probability that they are real genomic islands. Eleven genomic islands were found to code for products involved in causing disease (virulence factors) or in resistance to antibiotics (resistance factors). This finding could be useful for research on the pathogenicity of these bacteria and helpful in the treatment of the diseases that they cause. In a comparison of the distribution of mobility elements in genomic islands predicted by different methods, the Z-Island method gave lower false-positive rates. The Z-Island method was found to detect more known genomic islands than the two methods that we compared it with, SIGI-HMM and Island Pick. Furthermore, it maintained a better balance between specificity and sensitivity. The only inconvenience is that the steps for finding genomic islands by the Z-Island method are semi-automatic.