我看到的是一场比赛吗? 大致的帕林德罗姆导致了使用反向序列的基准指标中高估的假匹配率
George Glidden-Handgis1, Travis J Wheeler1
1R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, United States.
Bioinformatics advances
|May 20, 2024
概括
生物序列分析软件使用E值来评估匹配意义. 作为诱使用的反向序列,会因内部帕林德罗姆增加错误匹配率,这可能会影响灵敏度和下游分析.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 序列分析 序列分析
背景情况:
- 序列标记软件使用E值来估计与随机机会相匹配的意义.
- 具有重复区域的真实生物序列挑战了标准的E值评估.
- 反向生物序列越来越多地被用作评估序列对齐工具的诱.
研究的目的:
- 调查使用逆转生物序列作为序列对齐中的诱的影响.
- 了解序列之间的高得分对齐及其反转的现象.
- 评估这些发现对序列注释和蛋白质识别的影响.
主要方法:
- 对序列及其反向对应数之间的对齐分数的分析.
- 混合序列与反向序列对齐统计的比较.
- 评估内部palindromes对对齐分数的影响.
主要成果:
- 序列倾向于与它们的反转产生更高的对齐分数,而不是与无关的序列,即使在混合时.
- 这种现象归因于较长的平行符串比较较长的共同子字符串在混合序列的流行.
- 反向序列的对齐得分分布向右移动,增加了高得分的比赛.
结论:
- 通过反向序列诱高估错误匹配风险,可能导致不必要的高值和降低灵敏度.
- 反向序列应谨慎使用作为诱,需要删除真正数或接受潜在的夸大.
- 内部帕林德罗姆的患病率也可能会在基于质谱的蛋白质识别中增加错误发现率.
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