zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles
zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles
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DOI：
10.1101/gr.2129504
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发表时间：
2004-03-01
期刊：
影响因子：
7
通讯作者：
Stubbs, L
中科院分区：
文献类型：
--
作者：
Ovcharenko, I;Loots, GG;Stubbs, L
比较序列分析已发展成为识别在进化过程中保守的功能编码和非编码元件的所有基本技术。在这里，我们介绍 zPicture，这是一种基于 Web 的交互式序列比对和可视化工具，用于动态生成保护概况并识别进化保守区域 (ECR)。 zPicture 非常灵活，因为关键参数可以交互修改，允许用户在比较不同系统发育距离和进化速率的序列时差异预测 ECR。我们演示了该模块的应用来识别 HOXD 基因座中的已知调控元件，在高度保守的基因组背景下很难辨别功能性 ECR。 zPicture 还可以通过 rVista 工具门户促进转录因子结合位点分析。我们展示了一个 HBB 复合物的例子，当 zPicture/rVista 组合特异性地定位到两个含有 GATA-1、NF-E2 和 TAL1/E47 结合位点的 ECR 时，这些结合位点先前被鉴定为转录增强子。此外，zPicture 还链接到 UCSC 基因组浏览器，允许用户自动提取任何记录基因座的序列和基因注释。最后，我们描述了如何将该工具有效地应用于非脊椎动物基因组的分析，包括微生物的基因组。
Comparative sequence analysis has evolved as all essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, all interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing Users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, ill which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing Users to automatically extract Sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.