一种有效的顺序和并行的种植模体搜索算法
Efficient Sequential and Parallel Algorithms for Planted Motif Search
摘要：
模体搜索是检测一组DNA或蛋白质序列中发生的罕见事件的重要步骤。该问题的一种表述被称为（l，d）-基序搜索或种植基序搜索（PMS）。在PMS中，我们给出两个整数l和d以及n个生物序列。我们想找到所有长度为l的序列，这些序列出现在每个输入序列中，最多有d个错配。PMS问题是NP完全问题。PMS算法通常在被认为具有挑战性的某些情况下进行评估。本文提出了一种精确并行PMS算法PMS 8。PMS 8是第一个解决具有挑战性的（l，d）实例（25，10）和（26，11）的算法。PMS 8在具有较大l和d的实例上也是有效的，例如（50，21）。本文还介绍了3个l-聚体有一个共同d-近邻的充要条件。
英文摘要：
Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. This paper presents an exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). This paper also introduces necessary and sufficient conditions for 3 l-mers to have a common d-neighbor.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
