PMS6: A fast algorithm for motif discovery

Author

Bandyopadhyay, Shibdas ; Sahni, Sartaj ; Rajasekaran, Sanguthevar

Author_Institution

Dept. of CISE, Univ. of Florida, Gainesville, FL, USA

fYear

2012

fDate

23-25 Feb. 2012

Firstpage

1

Lastpage

6

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.

Keywords

biology computing; molecular biophysics; molecular configurations; (l,d)-motif discovery problem; PMS6; Approximation algorithms; Approximation methods; Complexity theory; Educational institutions; Hamming distance; Heuristic algorithms; Reflective binary codes; Planted motif search; string algorithms;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Advances in Bio and Medical Sciences (ICCABS), 2012 IEEE 2nd International Conference on

Conference_Location

Las Vegas, NV

Print_ISBN

978-1-4673-1320-9

Electronic_ISBN

978-1-4673-1319-3

Type

conf

DOI

10.1109/ICCABS.2012.6182627

Filename

6182627