Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
PLoS One. 2012;7(1):e28272. doi: 10.1371/journal.pone.0028272. Epub 2012 Jan 4.
Chromatin Immuno Precipitation (ChIP) profiling detects in vivo protein-DNA binding, and has revealed a large combinatorial complexity in the binding of chromatin associated proteins and their post-translational modifications. To fully explore the spatial and combinatorial patterns in ChIP-profiling data and detect potentially meaningful patterns, the areas of enrichment must be aligned and clustered, which is an algorithmically and computationally challenging task. We have developed CATCHprofiles, a novel tool for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns "ab initio", and enables the detection of new patterns from ChIP data at a high resolution, exemplified by the detection of asymmetric histone and histone modification patterns around H2A.Z-enriched sites. CATCHprofiles' capability for exhaustive analysis combined with its ease-of-use makes it an invaluable tool for explorative research based on ChIP profiling data. CATCHprofiles and the CATCH algorithm run on all platforms and is available for free through the CATCH website: http://catch.cmbi.ru.nl/. User support is available by subscribing to the mailing list catch-users@bioinformatics.org.
染色质免疫沉淀（ChIP）分析可检测体内蛋白质与 DNA 的结合，揭示了染色质相关蛋白与其翻译后修饰的结合具有很大的组合复杂性。为了充分探索 ChIP 分析数据中的空间和组合模式，并检测潜在的有意义模式，必须对富集区域进行对齐和聚类，这是一项具有挑战性的算法和计算任务。我们开发了 CATCHprofiles，这是一种用于 ChIP 分析数据中穷尽模式检测的新工具。CATCHprofiles 建立在用于 ChIP 分析数据的穷举对齐和层次聚类的高效计算实现之上。该工具具有一个图形界面，用于检查和浏览聚类结果。CATCHprofiles 不需要关于功能位点的先验知识，“从头开始”检测已知的结合模式，并能够从 ChIP 数据中以高分辨率检测新的模式，例如在富含 H2A.Z 的位点周围检测到不对称的组蛋白和组蛋白修饰模式。CATCHprofiles 的穷举分析能力与其易用性相结合，使其成为基于 ChIP 分析数据的探索性研究的宝贵工具。CATCHprofiles 和 CATCH 算法可在所有平台上运行，并可通过 CATCH 网站免费获得：http://catch.cmbi.ru.nl/。用户可通过订阅邮件列表 catch-users@bioinformatics.org 获得用户支持。
