使用序列和结构信息与树分解重建多个家族的祖先非编码RNA
Songdi Hu1, Vladimir Reinharz2, Olivier Tremblay-Savard1
1Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada.
概括
由于结构性保护,重建祖先RNA序列是很困难的. 这项研究引入了一种使用树分解的改进方法,以准确推断祖先非编码RNA (ncRNA) 序列,即使具有多个祖先结构.
科学领域:
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
- 分子进化分子进化
背景情况:
- 祖先非编码RNA (ncRNA) 序列重建具有挑战性,因为进化压力有利于结构,而不是序列的保存.
- 以前的方法经常产生比其后代更稳定的祖先序列,从而产生了矛盾.
- RNA家族可能从具有多个功能和多稳定的结构的祖先分子进化,随后是重复和子专业化.
研究的目的:
- 为了提高祖先ncRNA序列重建的准确性和减少模糊性.
- 为了解决假定祖先ncRNAs单一保存结构的方法的局限性.
- 开发一种能够从相关的ncRNA家族推断出祖先序列的方法,这些序列起源于具有多个功能的单个祖先分子.
主要方法:
- 开发了一种改进的祖先重建方法,利用树分解算法.
- 将更多的约束和立场纳入重建过程中.
- 用一个更现实的能量模型进行序列评估.
主要成果:
- 在模拟数据集上的祖先序列推理准确度显著改善.
- 减少了几个数量级推断的最佳祖先序列的数量.
- 在真实数据集 (RFam 族群 Glm 和 FinP-traJ) 上,新方法推断出较少,与以前的方法相比,结构更适合的祖先序列.
结论:
- 增强型树分解方法为重建祖先的ncRNA序列提供了更准确,更少含糊的方法.
- 这种方法有效地处理了祖先的ncRNAs拥有多个功能和结构的场景.
- 这些发现对了解ncRNA家族的进化历史及其功能多样化有意义.
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