评估用于检测蛋白质编码序列的计算工具:它们能完成任务吗?
D J Champion1, Ting-Hsuan Chen2, Susan Thomson3
1University of Otago.
概括
许多用于检测蛋白质编码基因的生物信息工具都是不可靠和低效的. 这项研究揭示了当前注释工具的重大局限性,强调需要改进基因组和转录组分析的方法.
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:
- 精确检测蛋白质编码基因对于理解基因组和转录组功能至关重要.
- 广泛使用的基因注释生物信息工具的可靠性在很大程度上仍未得到验证.
研究的目的:
- 评估新型蛋白质编码检测工具的准确性和效率.
- 为了比较核酸序列和基于对齐的方法的性能.
主要方法:
- 使用独立的对照评估了九种新的蛋白质编码检测工具.
- 使用编码外子作为正集合和长度匹配的跨基因/杂乱序列作为负集合.
- 将工具性能与一个纯粹的评分方案进行比较.
主要成果:
- 几种广泛使用的工具的准确性和计算效率都很差.
- 在9个工具中,只有3个明显超过了纯粹的评分方案.
- 基于对齐的方法在单个序列方法上显示出显著的优势.
结论:
- 现有的蛋白质编码注释工具具有显著的局限性,影响lncRNA注释.
- 对于培训和评估基因识别工具的更强大,更有效的方法有着至关重要的需求.
- 这项研究倡导先进的比较基因组方法和改进的基因组注释策略.
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