欢迎来到大叶子:改善非模型植物基因组中的基因组注释的最佳实践
Vidya S Vuruputoor1, Daniel Monyak1, Karl C Fetter1
1Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut 06269 USA.
Applications in plant sciences
|August 21, 2023
概括
评估植物基因组注释需要强大的基准. 结合基于证据的和ab initio的方法,包括短时间和长时间的阅读,然后进行后处理,可以获得最佳的蛋白质编码基因预测.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 细胞基因组注释缺乏强大的质量和完整性评估标准.
- 植物基因组注释是具有挑战性的,因为大尺寸,可转换的元素,和 ploidy 变异.
- 当前的注释软件往往缺乏基准测试,特别是对于非模型生物.
研究的目的:
- 研究基因组质量,复杂性,序列读取输入和方法论对植物蛋白编码基因预测的影响.
- 评估和推植物基因组注释的最佳实践.
- 为评估基因组注释准确性开发更强大的指标.
主要方法:
- 检查了重复掩盖,长读和短读输入以及 de novo 与基因组引导蛋白质证据的影响.
- 用BRAKER和MAKER的工作流程对五种植物基因组进行了利用.
- 对结构特征和序列相似性的基准标注.
主要成果:
- 包括基因结构和相似性对齐在内的基因基因基因和相似性对齐提供了更完整的准确性视图.
- 来自RNA读取对齐的转录单独不足以准确的基因组注释.
- 结合短阅读和长阅读可以改善注释;然而,添加蛋白质证据可以增加错误阳性,需要后处理.
结论:
- 建议使用结合基于证据和初步方法的基因预测工作流程.
- 短读和长读的组合,以及功能和结构后处理过器,对于最佳的植物基因组注释至关重要.
- 开发可靠的指标对于评估植物基因组注释质量和完整性至关重要.
关键词:
布雷克尔 (BRAKER) 是一个非常有价值的品牌.制造商是一个制造商.字符串Tie2 的字符串.塞布拉 (TSEBRA) 是一个基因鉴定 基因鉴定 基因鉴定基因组注释 基因组注释植物基因组的植物基因组.更多相关视频
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