Florea Liliana, McClelland Michael, Riemer Cathy, Schwartz Scott, Miller Webb
Informatics Research, Celera/Applied Biosystems, 45 W. Gude Drive, Rockville, MD 20850, USA.
Nucleic Acids Res. 2003 Jul 1;31(13):3527-32. doi: 10.1093/nar/gkg551.
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.
我们介绍了EnteriX，这是一套基于网络的可视化工具，共三个，用于以图形方式描绘来自相关肠杆菌种的几个固定序列和用户提供序列之间比对的比对信息，这些比对信息以一个参考基因组为锚定（http://bio.cse.psu.edu/）。第一个可视化工具Enteric展示参考基因组与每种相关细菌之间的堆叠式双序列比对，以PIPs（百分比一致性图）的形式示意性呈现。视图中编码了大规模基因组重排事件和功能标记。第二个可视化工具Menteric计算并展示序列核苷酸水平多重比对的1 Kb视图，以及基因、调控位点和保守区域的注释。第三个是名为Maj的基于Java的工具，以大致对应Enteric和Menteric视图的两种格式显示比对信息，并增加了放大功能。此类工具的用途多种多样，从检查多重序列比对以推断具有潜在调控作用的保守位点，到审视基因组之间在致病性或系统发育研究方面的共性和差异。EnteriX套件目前包含超过15个肠杆菌基因组，生成以四个不同锚定基因组为中心的视图，并支持在比对中纳入用户序列。
