Brown Daniel G, Truszkowski Jakub
David R. Cheriton School of Computer Science, University of Waterloo, Waterloo ON N2L 3G1, Canada.
Pac Symp Biocomput. 2013:310-9.
We consider the problem of phylogenetic placement, in which large numbers of sequences (often next-generation sequencing reads) are placed onto an existing phylogenetic tree. We adapt our recent work on phylogenetic tree inference, which uses ancestral sequence reconstruction and locality-sensitive hashing, to this domain. With these ideas, new sequences can be placed onto trees with high fidelity in strikingly fast runtimes. Our results are two orders of magnitude faster than existing programs for this domain, and show a modest accuracy tradeoff. Our results offer the possibility of analyzing many more reads in a next-generation sequencing project than is currently possible.
我们考虑系统发育定位问题，即在这个问题中，大量序列（通常是二代测序 reads）被定位到现有的系统发育树上。我们将近期关于系统发育树推断的工作（该工作使用祖先序列重建和局部敏感哈希）应用于这个领域。基于这些理念，新序列能够以惊人的快速运行时间被高精度地定位到树上。我们的结果比该领域现有的程序快两个数量级，并且显示出适度的准确性权衡。我们的结果为在二代测序项目中分析比目前更多的 reads 提供了可能性。
