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**1 - 4**of**4**### Solving Planted Motif Problem Using Modeling Method

"... Abstract- In this paper we describe a new method for solving the Planted Motif Problem that has applications in computational biology. A number of algorithms to solve this problem have been proposed in the past. The largest problem reported solved in the literature is (21, 8). Using the new method w ..."

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Abstract- In this paper we describe a new method for solving the Planted Motif Problem that has applications in computational biology. A number of algorithms to solve this problem have been proposed in the past. The largest problem reported solved in the literature is (21, 8). Using the new method we have solved much larger problems, up to a size of (48, 12). The new method is also much faster, and we compare its performance with the best performances reported in the literature.

### PMS6MC: A Multicore Algorithm for Motif Discovery

"... Abstractâ€”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 al ..."

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Abstractâ€”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. Keywords-Planted motif search, parallel string algorithms, multi-core algorithms. I.

### Article PMS6MC: A Multicore Algorithm for Motif Discovery

, 2013

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### Solving Planted Motif Problem on GPU

"... (l, d) planted motif problem is defined as: Given a sequence of n DNA sequences, each of length L, find M, the set of sequences(or motifs) of length l which have at-least one d-neighbor in each of the n sequences. Planted motif problem is an important and well-studied problem in computational biolog ..."

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(l, d) planted motif problem is defined as: Given a sequence of n DNA sequences, each of length L, find M, the set of sequences(or motifs) of length l which have at-least one d-neighbor in each of the n sequences. Planted motif problem is an important and well-studied problem in computational biology. Motif finding is useful for developing methods to obtain transcription factor binding sites, sequence classifica-tion, in developing methods for building phylogenetic trees etc. The planted motif problem is difficult to solve espe-cially for challenging instance sizes (15,5), (17,6), (19,7), and (21,8). The challenging instances are computationally intensive and require large amount of memory. Several serial implementations have been proposed for solving this prob-lem. The time required by these methods for solving large challenge instances is prohibitively expensive. In this paper, we propose a parallel implementation on GPU that solves the challenge instance (21,8) in 1.1 hours. We are not aware of any sequential or parallel method that will solve this chal-lenge instance in better time. Additionally, to the best our knowledge we are not aware of any previous implementation of a parallel method to solve the planted motif problem on GPU. 1.