Contreras-Moreira Bruno, Sebastian Alvaro
Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, Zaragoza, 50059, Spain.
Fundación ARAID, Zaragoza, Spain.
Methods Mol Biol. 2016;1482:259-77. doi: 10.1007/978-1-4939-6396-6_17.
FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyses.
足迹数据库（FootprintDB）是一个数据库和搜索引擎，它汇集了来自经过整理的DNA顺式元件和基序的开放获取文库及其相关转录因子（TFs）的调控序列。它通过利用存于蛋白质数据库中的蛋白质-DNA复合物，系统地注释转录因子的结合界面。因此，足迹数据库中的每个条目都是一个与已知能识别它的转录因子的蛋白质序列相关联的DNA基序，并且在大多数情况下，还包括参与特异性识别的预测界面残基集。本章逐步解释如何在足迹数据库中搜索DNA基序和蛋白质序列，以及如何将搜索聚焦于特定生物体。展示了两个实际应用案例，其中使用该软件分析植物中的转录调控。对结果进行了描述，旨在指导用户进行解读，并特别关注用户在进行类似分析时可能面临的选择。
