Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint
Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint
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DOI：
10.1016/j.resmic.2007.08.005
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发表时间：
2007-10-01
影响因子：
2.6
通讯作者：
Timms, Peter
中科院分区：
文献类型：
--
作者：
Grech, Brian;Maetschke, Stefan;Timms, Peter
目前，缺乏可以利用同一细菌属内不同物种的多个全基因组序列的系统发育足迹程序。因此，我们已经开发并测试了一种名为Footy的基于位置权重矩阵的程序，该程序对细菌基因组进行全基因组分析，以寻找具有遗传足迹的启动子。当Footy被用来分析来自三种衣原体物种的基因上游的非编码区的启动子时，它预测了总共42个启动子，其中41个是新的。Footy预测的41个新启动子中的10个在沙眼衣原体中通过定位相关基因转录本的5'端进行生物学分析。引物延伸测定验证了10个启动子中的7个。当Footy与其他两种公认的细菌启动子全基因组预测方法（标准PWM方法和MITRA）进行比较时，Footy的表现与这些程序一样好或更好。因此，本文显示了生物信息学程序的价值，该程序能够对细菌的启动子进行全基因组分析。(C)2007年，Elsevier Masson SAS。All rights reserved.
Currently, there is a lack of phylogenetic footprinting programmes that can take advantage of multiple whole genome sequences of different species within the same bacterial genus. Therefore, we have developed and tested a position weight matrix-based programme called Footy, that performs genome-wide analysis of bacterial genomes for promoters that phylogenetically footprint. When Footy was used to analyse the non-coding regions upstream of genes from three chlamyidal species for promoters that phylogenetically footprint, it predicted a total of 42 promoters, of which 41 were new. Ten of the 41 new promoters predicted by Footy were biologically assayed in Chlamydia trachomatis by mapping the 5' end of the transcripts for the associated genes. The primer extension assay validated seven of the 10 promoters. When Footy was compared to two other accepted methods for genome-wide prediction of promoters in bacteria (the standard PWM method and MITRA), Footy performed equally as well or better than these programmes. This paper, therefore, shows the value of a bioinformatics programme able to perform genome-wide analysis of bacteria for promoters that phylogenetically footprint. (C) 2007 Elsevier Masson SAS. All rights reserved.