PMS6: A Fast Algorithm for Motif Discovery.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences Pub Date : 2012-01-01 DOI:10.1109/ICCABS.2012.6182627

Shibdas Bandyopadhyay, Sartaj Sahni, Sanguthevar Rajasekaran

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Abstract

We propose a new algorithm, PMS6, for the (l, d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. The run time ratio PMS5/PMS6, where PMS5 is the fastest previously known algorithm for motif discovery in large instances, ranges from a high of 2.20 for the (21,8) challenge instances to a low of 1.69 for the (17,6) challenge instances. Both PMS5 and PMS6 require some amount of preprocessing. The preprocessing time for PMS6 is 34 times faster than that for PMS5 for (23,9) instances. When preprocessing time is factored in, the run time ratio PMS5/PMS6 is as high as 2.75 for (13,4) instances and as low as 1.95 for (17,6) instances.

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PMS6：一种快速的动机发现算法。

我们针对(l, d)-motif发现问题提出了一种新算法PMS6，在这个问题中，我们要找到所有长度为l的字符串，这些字符串出现在一组给定字符串中的每一个字符串中，且最多有d个错配。PMS5/PMS6 的运行时间比从 (21,8) 挑战实例的最高 2.20 到 (17,6) 挑战实例的最低 1.69 不等，其中 PMS5 是之前已知的在大型实例中发现主题的最快算法。PMS5 和 PMS6 都需要一定的预处理。在(23,9)实例中，PMS6 的预处理时间比 PMS5 快 34 倍。如果将预处理时间考虑在内，PMS5/PMS6 的运行时间比在(13,4)实例中高达 2.75，而在(17,6)实例中则低至 1.95。

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IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences

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