Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models
Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models
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DOI：
10.1093/nar/30.6.1418
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发表时间：
2002-03-15
影响因子：
14.9
通讯作者：
Bessières, P
中科院分区：
文献类型：
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作者：
Nicolas, P;Bize, L;Bessières, P
我们在这里提出了一种新的统计分割方法对枯草芽孢杆菌染色体序列的使用。隐马尔可夫模型的最大似然参数估计，期望最大化算法的基础上，使之能够分割的DNA序列，根据其本地组成。这种方法不是基于滑动窗口;它使不同的组合类能够分离，而无需事先知道它们的内容，大小和本地化。我们比较了这些组成类，从序列中获得的，与注释的DNA物理图谱，序列同源性和重复区域。揭示的第一异质性区分两个编码链和非编码区。其他主要的异质性出现;一些与水平基因转移有关，一些与疏水性蛋白质编码链的t富集组成有关，而另一些与高表达基因的密码子使用适合性有关。关于潜在的和已建立的基因转移，我们发现了9个已知的前噬菌体，加上14个新的区域的非典型组成。它们中的一些被重复序列包围，大多数基因功能未知或与继发性catalysis、金属和抗生素抗性相关基因具有同源性。令人惊讶的是，我们注意到所有这些检测到的区域都比宿主基因组丰富，这就提出了它们的远程来源问题。
We present here the use of a new statistical segmentation method on the Bacillus subtilis chromosome sequence. Maximum likelihood parameter estimation of a hidden Markov model, based on the expectation-maximization algorithm, enables one to segment the DNA sequence according to its local composition. This approach is not based on sliding windows; it enables different compositional classes to be separated without prior knowledge of their content, size and localization. We compared these compositional classes, obtained from the sequence, with the annotated DNA physical map, sequence homologies and repeat regions. The first heterogeneity revealed discriminates between the two coding strands and the non-coding regions. Other main heterogeneities arise; some are related to horizontal gene transfer, some to t-enriched composition of hydrophobic protein coding strands, and others to the codon usage fitness of highly expressed genes. Concerning potential and established gene transfers, we found 9 of the 10 known prophages, plus 14 new regions of atypical composition. Some of them are surrounded by repeats, most of their genes have unknown function or possess homology to genes involved in secondary catabolism, metal and antibiotic resistance. Surprisingly, we notice that all of these detected regions are a + t-richer than the host genome, raising the question of their remote sources.