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"Efficient Sequential And Parallel Algorithms For Planted Motif Search." and the language of the book is English.


“Efficient Sequential And Parallel Algorithms For Planted Motif Search.” Metadata:

  • Title: ➤  Efficient Sequential And Parallel Algorithms For Planted Motif Search.
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  • Language: English

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  • Internet Archive ID: pubmed-PMC3924400

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This article is from <a href="//archive.org/search.php?query=journaltitle%3A%28BMC%20Bioinformatics%29" rel="ugc nofollow">BMC Bioinformatics</a>, <a href="//archive.org/search.php?query=journaltitle%3A%28BMC%20Bioinformatics%29%20AND%20volume%3A%2815%29" rel="ugc nofollow">volume 15</a>.<h2>Abstract</h2>Background: 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. Despite ample research in the area, a considerable performance gap exists because many state of the art algorithms have large runtimes even for moderately challenging instances. Results: This paper presents a fast 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). We include a comparison of PMS8 with several state of the art algorithms on multiple problem instances. This paper also presents necessary and sufficient conditions for 3 l-mers to have a common d-neighbor. The program is freely available at http://engr.uconn.edu/~man09004/PMS8/. Conclusions: We present PMS8, an efficient exact algorithm for Planted Motif Search. PMS8 introduces novel ideas for generating common neighborhoods. We have also implemented a parallel version for this algorithm. PMS8 can solve instances not solved by any previous algorithms.

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