An efficient algorithm for Perfect Phylogeny Haplotyping.

Ravi Vijayasatya, Amar Mukherjee
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引用次数: 7

Abstract

The Perfect Phylogeny Haplotyping (PPH) problem is one of the many computational approaches to the Haplotype Inference (HI) problem. Though there are many O(nm(2)) solutions to the PPH problem, the complexity of the PPH problem itself has remained an open question. In this paper, We introduce the FlexTree data structure that represents all the solutions for a PPH instance. We also introduce row-ordering that arranges the genotypes in a more manageable fashion. The column ordering, the FlexTree data structure and the row ordering together make the O(nm) OPPH algorithm possible. We also present some results on simulated data which demonstrate that the OPPH algorithm performs quiet impressively when compared to the earlier O(nm(2)) algorithms.

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完美系统发育单倍型的高效算法。
完美系统发育单倍型(PPH)问题是解决单倍型推断(HI)问题的众多计算方法之一。虽然PPH问题有许多0 (nm(2))的解决方案,但PPH问题本身的复杂性仍然是一个悬而未决的问题。在本文中,我们介绍了代表PPH实例的所有解决方案的FlexTree数据结构。我们还介绍了以更易于管理的方式排列基因型的行排序。列排序、FlexTree数据结构和行排序共同使O(nm) OPPH算法成为可能。我们还提供了一些模拟数据的结果,这些结果表明,与早期的O(nm(2))算法相比,OPPH算法的性能令人印象深刻。
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