RSAT::植物：植物基因组上游序列簇中的基序发现

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.

作者信息

Contreras-Moreira Bruno, Castro-Mondragon Jaime A, Rioualen Claire, Cantalapiedra Carlos P, van Helden Jacques

机构信息

Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, 50059, Zaragoza, Spain.

Fundación ARAID, calle María de Luna 11, 50018, Zaragoza, Spain.

出版信息

Methods Mol Biol. 2016;1482:279-95. doi: 10.1007/978-1-4939-6396-6_18.

DOI:10.1007/978-1-4939-6396-6_18

PMID:27557774

Abstract

The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, and pattern matching. RSAT::Plants also integrates the footprintDB collection of DNA motifs. This protocol explains step-by-step how to discover DNA motifs in regulatory regions of clusters of co-expressed genes in plants. It also explains how to empirically control the significance of the result, and how to associate the discovered motifs with putative binding factors.

摘要

调控序列分析工具（RSAT，http://plants.rsat.eu ）的植物专用镜像为研究植物转录调控的人员提供了专门的选项。该网站包含来自Ensembl Plants和其他来源（目前有40个）定期更新的物种全测序基因组，并支持分析调控序列时经常需要的一系列任务，如检索上游序列、基序发现、基序比较和模式匹配。RSAT::Plants还整合了DNA基序的footprintDB集合。本方案逐步解释了如何在植物共表达基因簇的调控区域中发现DNA基序。它还解释了如何凭经验控制结果的显著性，以及如何将发现的基序与假定的结合因子相关联。