PMS6MC: A Multicore Algorithm for Motif Discovery
| Title: | PMS6MC: A Multicore Algorithm for Motif Discovery |
|---|---|
| Authors: | Shibdas Bandyopadhyay, Sartaj Sahni, Sanguthevar Rajasekaran |
| Source: | Algorithms, Vol 6, Iss 4, Pp 805-823 (2013) |
| Publisher Information: | MDPI AG, 2013. |
| Publication Year: | 2013 |
| Collection: | LCC:Industrial engineering. Management engineering LCC:Electronic computers. Computer science |
| Subject Terms: | planted motif search, parallel string algorithms, multi-core algorithms, Industrial engineering. Management engineering, T55.4-60.8, Electronic computers. Computer science, QA75.5-76.95 |
| More Details: | We develop an efficient multicore algorithm, PMS6MC, 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. PMS6MC is based on PMS6, which is currently the fastest single-core algorithm for motif discovery in large instances. The speedup, relative to PMS6, attained by our multicore algorithm ranges from a high of 6.62 for the (17,6) challenging instances to a low of 2.75 for the (13,4) challenging instances on an Intel 6-core system. We estimate that PMS6MC is 2 to 4 times faster than other parallel algorithms for motif search on large instances. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 1999-4893 |
| Relation: | http://www.mdpi.com/1999-4893/6/4/805; https://doaj.org/toc/1999-4893 |
| DOI: | 10.3390/a6040805 |
| Access URL: | https://doaj.org/article/5cb2223f74474e9fb8fd1174471b443e |
| Accession Number: | edsdoj.5cb2223f74474e9fb8fd1174471b443e |
| Database: | Directory of Open Access Journals |
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