Discovering Motifs in Biological Sequences Using the Micron Automata Processor
Discovering Motifs in Biological Sequences Using the Micron Automata Processor
复制标题
使用微米自动机处理器发现生物序列中的基序
DOI：
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
S. Aluru
中科院分区：
文献类型：
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作者：
Indranil Roy;S. Aluru
在多个DNA或蛋白质序列之间找到大约保守的序列，称为基序是计算生物学中的重要问题。在本文中，我们考虑了（L; d）基序搜索问题，即在至少n给定序列的至少q中识别一个或多个长度为l的基序，每种序列的发生与大多数替代的基序都不同。该问题已知是NP完整的，迄今为止报告的最大解决实例为（26; 11）。我们使用大量非确定性有限自动机（NFA）上的流执行（NFA）提出了一种针对（L; d）基序搜索问题的新型算法。该解决方案旨在利用微米自动机处理器，这是一种靠近部署的新技术，可以同时并行执行多个NFA。我们通过估计问题实例（39; 18）和（40; 17）的运行时间来证明（L; d）图案搜索问题的更大实例，以解决（L; d）图案搜索问题的更大实例。该论文是使用这种新的加速器技术解决问题的有用指南。
Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l; d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26;11). We propose a novel algorithm for the (l; d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l; d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39; 18) and (40; 17). The paper serves as a useful guide to solving problems using this new accelerator technology.
影响因子：
56.9
作者：
LAWRENCE, CE;ALTSCHUL, SF;WOOTTON, JC
通讯作者：
WOOTTON, JC