EchinoBase: Tools for Echinoderm Genome Analyses
EchinoBase: Tools for Echinoderm Genome Analyses
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DOI：
10.1007/978-1-4939-7737-6_12
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发表时间：
2018-01-01
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影响因子：
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通讯作者：
Hinman, Veronica F.
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文献类型：
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作者：
Cary, Gregory A.;Cameron, R. Andrew;Hinman, Veronica F.
棘皮动物是无脊椎动物后口动物门，构成了许多生物学学科的重要研究模型。 EchinoBase (www.echinobase.org) 是一个棘皮动物特异性基因组数据库和网络信息系统，为询问和探索棘皮动物基因组数据提供了一个平台。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，以方便使用这些数据进行快速查询（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。最后，我们提出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的观点。它们所允许的可用数据集和分析提供了了解棘皮动物基因组如何调控（尤其是在早期发育过程中）所需的基本组成部分，并为该门物种之间的比较基因组查询提供了平台。
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.