Literature DB >> 25309700

PMS6MC: A Multicore Algorithm for Motif Discovery.

Shibdas Bandyopadhyay1, Sartaj Sahni2, Sanguthevar Rajasekaran3.   

Abstract

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.

Entities:  

Keywords:  Planted motif search; multi-core algorithms; parallel string algorithms

Year:  2013        PMID： 25309700      PMCID： PMC4193679          DOI： 10.3390/a6040805

Source DB:  PubMed          Journal:  Algorithms        ISSN： 1999-4893


  15 in total

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Authors:  Hieu Dinh; Sanguthevar Rajasekaran; Vamsi K Kundeti
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9.  Efficient motif finding algorithms for large-alphabet inputs.

Authors:  Pavel P Kuksa; Vladimir Pavlovic
Journal:  BMC Bioinformatics       Date:  2010-10-26       Impact factor: 3.169

10.  A speedup technique for (l, d)-motif finding algorithms.

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Journal:  BMC Res Notes       Date:  2011-03-08
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