Scripting Analyses of Genomes in Ensembl Plants.
Scripting Analyses of Genomes in Ensembl Plants.
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DOI：
10.1007/978-1-0716-2067-0_2
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Flicek P
中科院分区：
文献类型：
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作者：
Contreras-Moreira B;Naamati G;Rosello M;Allen JE;Hunt SE;Muffato M;Gall A;Flicek P
Ensembl Plants（plants.ensembl.org）提供植物基因组规模的信息，每年发布四次。截至第47版（2020年4月），它包含79个物种，包括基因组序列，基因模型和功能注释。比较分析有助于重建基因家族、基因组和多倍体基因组组成的进化历史。一些物种有基因表达基线报告或基因型间的变异。虽然可以通过Ensembl基因组浏览器访问数据，但在这里我们特别回顾了如何以编程方式查询我们的植物基因组并批量下载数据。对于其他非植物物种，包括植物病原体、害虫和传粉者，这些进入途径在整个Ensembl通常是一致的。
Ensembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.