Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol
Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol
复制标题
果蝇物种内基因的手动注释：基因组学教育合作协议
DOI：
10.1101/2020.12.10.420521
复制
发表时间：
2020
期刊：
影响因子：
--
通讯作者：
L. Reed
中科院分区：
文献类型：
--
作者：
Chinmay P. Rele;Katie M. Sandlin;Wilson Leung;L. Reed
注释多种生物体的基因组使我们能够研究它们的基因以及这些基因的进化。虽然许多真核基因组组装已经包括计算基因预测，但这些预测可以受益于通过手动基因注释进行的审查和完善。基因组学教育合作伙伴关系（GEP；thegep.org）开发了蛋白质编码基因注释协议，使本科生和其他研究人员能够创建可用于后续科学研究的高质量基因注释。例如，GEP 教师已利用该方案让本科生使用黑腹果蝇作为信息基因组，对 28 种果蝇物种中涉及胰岛素信号通路的基因进行比较注释。学生使用多行计算和实验证据构建基因模型，包括表达数据（例如 RNA-Seq）、序列相似性（例如 BLAST、多序列比对）和计算基因预测。为了进行质量控制，每个基因都由至少两名独立工作的学生进行注释，然后由一名更有经验的学生对提交的基因模型进行协调。本文概述了注释协议，并描述了如何解决学生提交的基因模型中的差异，以产生适合后续分析的最终高质量基因集。该注释协议可以适应其他科学问题（例如，果蝇 Muller F 元件的扩展）和其他物种（例如，寄生蜂），为本科生参与基因组学研究提供额外的机会。这些学生的注释工作可以大大提高公开基因组数据库中基因注释的质量。
Annotating the genomes of multiple organisms allows us to study their genes as well as the evolution of those genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; thegep.org) has developed an annotation protocol for protein-coding genes that enables undergraduate students and other researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 28 Drosophila species, using D. melanogaster as the informant genome. Students construct gene models using multiple lines of computational and experimental evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST, multiple sequence alignments), and computational gene predictions. For quality control, each gene is annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. This annotation protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and other species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.
影响因子：
12.3
作者：
Kovaka, Sam;Zimin, Aleksey, V;Pertea, Mihaela
通讯作者：
Pertea, Mihaela
DOI：
10.1007/978-1-4939-9173-0_5
发表时间：
2019-01-01
期刊：
GENE PREDICTION: METHODS AND PROTOCOLS
影响因子：
--
作者：
Hoff, Katharina J.;Lomsadze, Alexandre;Stanke, Mario
通讯作者：
Stanke, Mario