Florea L, Riemer C, Schwartz S, Zhang Z, Stojanovic N, Miller W, McClelland M
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
Nucleic Acids Res. 2000 Sep 15;28(18):3486-96. doi: 10.1093/nar/28.18.3486.
With the increase in the flow of sequence data, both in contigs and whole genomes, visual aids for comparison and analysis studies are becoming imperative. We describe three web-based tools for visualizing alignments of bacterial genomes. The first, called Enteric, produces a graphical, hypertext view of pairwise alignments between a reference genome and sequences from each of several related organisms, covering 20 kb around a user-specified position. Insertions, deletions and rearrangements relative to the reference genome are color-coded, which reveals many intriguing differences among genomes. The second, Menteric, computes and displays nucleotide-level multiple alignments of the same sequences, together with annotations of ORFs and regulatory sites, in a 1 kb region surrounding a given address. The third, a Java-based viewer called Maj, combines some features of the previous tools, and adds a zoom-in mechanism. We compare the Escherichia coli K-12 genome with the partially sequenced genomes of Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, and the Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A. Examination of the pairwise and multiple alignments in a region allows one to draw inferences about regulatory patterns and functional assignments. For example, these tools revealed that rffH, a gene involved in enterobacterial common antigen (ECA) biosynthesis, is partly deleted in one of the genomes. We used PCR to show that this deletion occurs sporadically in some strains of some serovars of S.enterica subspecies I but not in any strains tested from six other subspecies. The resulting cell surface diversity may be associated with selection by the host immune response.
随着重叠群和全基因组序列数据流量的增加，用于比较和分析研究的可视化辅助工具变得势在必行。我们描述了三种用于可视化细菌基因组比对的基于网络的工具。第一种称为Enteric，它生成参考基因组与几种相关生物体中每一个的序列之间的成对比对的图形化超文本视图，覆盖用户指定位置周围20 kb的区域。相对于参考基因组的插入、缺失和重排用颜色编码，这揭示了基因组之间许多有趣的差异。第二种，Menteric，计算并显示相同序列的核苷酸水平多重比对，以及在给定地址周围1 kb区域内的开放阅读框（ORF）和调控位点的注释。第三种，一个名为Maj的基于Java的查看器，结合了前两种工具的一些功能，并添加了放大机制。我们将大肠杆菌K-12基因组与肺炎克雷伯菌、鼠疫耶尔森菌、霍乱弧菌以及肠炎沙门氏菌血清型鼠伤寒沙门氏菌、伤寒沙门氏菌和甲型副伤寒沙门氏菌的部分测序基因组进行了比较。检查一个区域内的成对和多重比对可以让人推断出调控模式和功能分配。例如，这些工具显示，参与肠杆菌共同抗原（ECA）生物合成的基因rffH在其中一个基因组中部分缺失。我们使用聚合酶链反应（PCR）表明，这种缺失在肠炎沙门氏菌亚种I的一些血清型的某些菌株中偶尔出现，但在其他六个亚种测试的任何菌株中都没有出现。由此产生的细胞表面多样性可能与宿主免疫反应的选择有关。
