PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.
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DOI：
10.1093/nar/gkx1002
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Vandepoele K
中科院分区：
文献类型：
--
作者：
Van Bel M;Diels T;Vancaester E;Kreft L;Botzki A;Van de Peer Y;Coppens F;Vandepoele K
PLAZA （https://bioinformatics.psb.ugent.be/plaza）是一个以植物为导向的比较、进化和功能基因组学在线资源。PLAZA平台由多个独立的实例组成，专注于不同的植物分支，同时也提供了一组一致的参考物种。每个PLAZA实例包含结构和功能基因注释，基因家族数据和系统发育树以及详细的基因共线性信息。用户友好的web界面使必要的工具和可视化可访问，特定于每个数据类型。这里我们介绍PLAZA 4.0，它是PLAZA框架的最新版本。该版本包含两个新实例（Dicots 4.0和Monocots 4.0），提供了大量新可用物种，并提供对更新和新实现的工具和可视化的访问，帮助用户满足日益增长的复杂和深入分析的需求。两个样地的物种总数几乎翻了一番，从PLAZA 3.0的37种增加到PLAZA 4.0的71种，其中作物物种（如小麦、棕榈油）和具有进化意义的物种（如云杉、红杉）的覆盖范围更广。新的PLAZA实例也可以通过RESTful web服务的编程接口访问，从而允许生物信息学家以最佳方式利用PLAZA平台的功能。
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.