Cary Gregory A, Cameron R Andrew, Hinman Veronica F
Department of Biological Sciences, Mellon Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Methods Mol Biol. 2018;1757:349-369. doi: 10.1007/978-1-4939-7737-6_12.
The echinoderms are a phylum of invertebrate deuterostome animals that constitute important research models for a number of biological disciplines. EchinoBase ( www.echinobase.org ) is an echinoderm-specific genome database and web information system that provides a platform for the interrogation and exploration of echinoderm genomic data. This chapter outlines the datasets available on EchinoBase; from assembled genomes and genome annotations, to spatial and quantitative expression data, as well as functional genomics datasets. We also highlight the bioinformatic tools available on the website to facilitate rapid inquiries using these data (genome browsers, precompiled BLAST databases, etc.), and suggest optimized strategies for performing these inquiries. We conclude with a perspective on how one could integrate various genomic resources to predict putative noncoding regulatory regions. The available datasets and analyses they permit provide the basic components required for developing an understanding of how echinoderm genomes are regulated, especially during early development, and provides a platform for comparative genomic inquiries among species in this phylum.
棘皮动物是一类无脊椎后口动物，是许多生物学学科的重要研究模型。EchinoBase（www.echinobase.org）是一个棘皮动物特有的基因组数据库和网络信息系统，为棘皮动物基因组数据的查询和探索提供了一个平台。本章概述了EchinoBase上可用的数据集；从组装的基因组和基因组注释，到空间和定量表达数据，以及功能基因组学数据集。我们还重点介绍了网站上可用的生物信息学工具，以促进对这些数据的快速查询（基因组浏览器、预编译的BLAST数据库等），并提出执行这些查询的优化策略。我们最后展望了如何整合各种基因组资源来预测假定的非编码调控区域。可用的数据集及其允许的分析提供了理解棘皮动物基因组如何调控（特别是在早期发育过程中）所需的基本组件，并为该门物种间的比较基因组查询提供了一个平台。
