A new algorithm for DNA sequence assembly.
A new algorithm for DNA sequence assembly.
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DOI：
10.1089/cmb.1995.2.291
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发表时间：
1995-01-01
期刊：
影响因子：
--
通讯作者：
Waterman, M S
中科院分区：
文献类型：
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作者：
Idury, R M;Waterman, M S
自1976年快速DNA测序方法问世以来，科学家们一直面临着从测序片段推断DNA序列的问题。鸟枪测序是一种在实践中应用的成熟的生物学和计算方法。许多传统的散弹枪测序算法是基于成对片段重叠的概念。虽然鸟枪测序根据重叠片段的序列推断DNA序列，但一种最新的互补方法，称为杂交测序（SBH），根据代表固定长度k的所有子词的寡聚物集推断DNA序列。在本文中，我们提出了一种新的DNA序列组装计算机算法，该算法以一种新颖的方式结合了鸟枪和SBH方法的技术。初步研究表明，该算法对DNA序列组装具有快速、实用的优点。
Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pairwise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH), infers a DNA sequence given the set of oligomers that represents all subwords of some fixed length, k. In this paper, we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises to be very fast and practical for DNA sequence assembly.