Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.
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Cinteny：多种生物体中同步和基因组重排的灵活分析和可视化。
DOI：
10.1186/1471-2105-8-82
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发表时间：
2007-03-08
影响因子：
3
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中科院分区：
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识别同线区域，即具有进化保守顺序的基因块或其他标记，并根据染色体重排来量化基因组之间的进化关联性是比较基因组学的中心目标之一。然而，共线分析和由此产生的基因组重排评估对影响共线区块检测的一些任意参数的选择是敏感的。特别是，需要评估一组标记的选择和不同聚集策略的效果，这些策略使得能够粗粒化共振块并排除微重排。因此，促进共轭序列鉴定、可视化和分析的现有工具和资源需要进一步改进，以便为这种分析提供一个灵活的平台，特别是在多基因组的背景下。我们提出了一个新的工具，Cteny，用于快速识别和分析具有不同标记集和不同水平的共线块粗粒化的共线。使用Hannenalli-Pevzner方法及其扩展，Cteny还能够根据重排的数量(逆转距离)交互地确定基因组之间的进化关系。具体来说，Cteny提供了：i)将同步浏览与多个基因组的进化距离评估相结合；ii)灵活地实时调整参数和重新计算结果；iii)能够使用用户提供的数据，例如同源基因、序列标签或其他保守的标记。此外，Cteny还提供了许多带注释的哺乳动物、无脊椎动物和真菌基因组，这些基因组已预先加载并可在上进行分析。Cteny使人们能够自动比较多个基因组，并为同步阻断检测和随后的反转距离计算执行敏感性分析。Cteny还可以用来交互浏览保存在多个基因组中的同线片段，促进基因组注释和新测序基因组组装的验证，以及构建和评估系统基因组树。
Identifying syntenic regions, i.e., blocks of genes or other markers with evolutionary conserved order, and quantifying evolutionary relatedness between genomes in terms of chromosomal rearrangements is one of the central goals in comparative genomics. However, the analysis of synteny and the resulting assessment of genome rearrangements are sensitive to the choice of a number of arbitrary parameters that affect the detection of synteny blocks. In particular, the choice of a set of markers and the effect of different aggregation strategies, which enable coarse graining of synteny blocks and exclusion of micro-rearrangements, need to be assessed. Therefore, existing tools and resources that facilitate identification, visualization and analysis of synteny need to be further improved to provide a flexible platform for such analysis, especially in the context of multiple genomes. We present a new tool, Cinteny, for fast identification and analysis of synteny with different sets of markers and various levels of coarse graining of syntenic blocks. Using Hannenhalli-Pevzner approach and its extensions, Cinteny also enables interactive determination of evolutionary relationships between genomes in terms of the number of rearrangements (the reversal distance). In particular, Cinteny provides: i) integration of synteny browsing with assessment of evolutionary distances for multiple genomes; ii) flexibility to adjust the parameters and re-compute the results on-the-fly; iii) ability to work with user provided data, such as orthologous genes, sequence tags or other conserved markers. In addition, Cinteny provides many annotated mammalian, invertebrate and fungal genomes that are pre-loaded and available for analysis at . Cinteny allows one to automatically compare multiple genomes and perform sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances. Cinteny can also be used to interactively browse syntenic blocks conserved in multiple genomes, to facilitate genome annotation and validation of assemblies for newly sequenced genomes, and to construct and assess phylogenomic trees.