EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
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DOI：
10.1093/nar/gkg551
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Miller, W
中科院分区：
文献类型：
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作者：
Florea, L;McClelland, M;Miller, W
我们描述了EnteriX，一套三个基于网络的可视化工具，用于图形化地描绘来自相关肠细菌物种的几个固定和用户提供的序列之间的比较的比对信息，锚定在参考基因组上（http：//bio.cse.psu.edu/）。第一个可视化，肠道，显示了参考基因组和每个相关细菌之间的堆叠成对比对，示意性地表示为PIP（百分比同一性图）。视图中编码的是大规模基因组重排事件和功能地标。第二个可视化，Menteric，计算和显示1 Kb的核苷酸水平的序列的多重比对，以及基因，调控位点和保守区的注释视图。第三个是一个名为Maj的基于Java的工具，它以两种格式显示对齐信息，大致对应于Enteric和Menteric视图，并添加了放大功能。这些工具的用途是多种多样的，从检查多序列比对来推断具有潜在调控作用的保守位点，到仔细检查致病性或系统发育研究的基因组之间的共性和差异。EnteriX套件目前包括>15个肠细菌基因组，生成以四个不同的锚基因组为中心的视图，并为在比对中包括用户序列提供支持。
We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.