Multiseed lossless filtration
Multiseed lossless filtration
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DOI：
10.1109/tcbb.2005.12
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发表时间：
2005-01-01
影响因子：
4.5
通讯作者：
Roytberg, M
中科院分区：
文献类型：
--
作者：
Kucherov, G;Noé, L;Roytberg, M
我们研究了一种基于种子的无损过滤方法，用于近似字符串匹配和相关的生物信息学应用。该方法基于同时使用几个间隔的种子，而不是Burkhardt和Karkkainen [1]研究的单个种子。我们提出了算法来计算种子家庭的几个重要参数，研究其组合特性，并描述了几种技术来构建有效的家庭。我们还报告了一个大规模的应用所提出的技术的EST序列数据库的寡核苷酸选择的问题。
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Karkkainen [1]. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.