### Abstract

We consider the planted (l,d)-motif search problem, which consists of finding a substring of length l that occurs in each s _{i} in a set of input sequences {s _{1},s _{t} } with at most d substitutions. In this paper, we study the effect of using Balla, Davila, and Rajasekaran strategy on voting algorithm practically. We call this technique, modified voting algorithm. We present an experimental study between original and modified voting algorithms on simulated data from (9,d) to (15,d). The comparison shows that the voting algorithm is faster than its modification in all instances except the instance (15,3). We also study the effect of increasing h, which is proposed by Balla, Davila, and Rajasekaran on the modified voting algorithm. From this study, we obtained the values of the number of sequences that make the running time of modified voting algorithm less than the voting algorithm and minimum. Finally, we analyze the experimental results and give some observations according to the relations: (1) l is fixed and d is variable. (2) l is variable and d is fixed. (3) l and d are variables. (4) (l,d) is challenging.

Original language | English |
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Title of host publication | Advances in Computational Biology |

Pages | 65-73 |

Number of pages | 9 |

DOIs | |

Publication status | Published - 1 Dec 2010 |

Externally published | Yes |

### Publication series

Name | Advances in Experimental Medicine and Biology |
---|---|

Volume | 680 |

ISSN (Print) | 0065-2598 |

### Fingerprint

### Keywords

- Binding site
- DNA motif
- Exact algorithm
- Planted (l,d)-motif
- Voting algorithm

### ASJC Scopus subject areas

- Medicine(all)
- Biochemistry, Genetics and Molecular Biology(all)

### Cite this

*Advances in Computational Biology*(pp. 65-73). (Advances in Experimental Medicine and Biology; Vol. 680). https://doi.org/10.1007/978-1-4419-5913-3_8

**Experimental study of modified voting algorithm for planted (l,d)-motif problem.** / Bahig, Hazem M.; Abbas, Mostafa; Bhery, Ashraf.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*Advances in Computational Biology.*Advances in Experimental Medicine and Biology, vol. 680, pp. 65-73. https://doi.org/10.1007/978-1-4419-5913-3_8

}

TY - GEN

T1 - Experimental study of modified voting algorithm for planted (l,d)-motif problem

AU - Bahig, Hazem M.

AU - Abbas, Mostafa

AU - Bhery, Ashraf

PY - 2010/12/1

Y1 - 2010/12/1

N2 - We consider the planted (l,d)-motif search problem, which consists of finding a substring of length l that occurs in each s i in a set of input sequences {s 1,s t } with at most d substitutions. In this paper, we study the effect of using Balla, Davila, and Rajasekaran strategy on voting algorithm practically. We call this technique, modified voting algorithm. We present an experimental study between original and modified voting algorithms on simulated data from (9,d) to (15,d). The comparison shows that the voting algorithm is faster than its modification in all instances except the instance (15,3). We also study the effect of increasing h, which is proposed by Balla, Davila, and Rajasekaran on the modified voting algorithm. From this study, we obtained the values of the number of sequences that make the running time of modified voting algorithm less than the voting algorithm and minimum. Finally, we analyze the experimental results and give some observations according to the relations: (1) l is fixed and d is variable. (2) l is variable and d is fixed. (3) l and d are variables. (4) (l,d) is challenging.

AB - We consider the planted (l,d)-motif search problem, which consists of finding a substring of length l that occurs in each s i in a set of input sequences {s 1,s t } with at most d substitutions. In this paper, we study the effect of using Balla, Davila, and Rajasekaran strategy on voting algorithm practically. We call this technique, modified voting algorithm. We present an experimental study between original and modified voting algorithms on simulated data from (9,d) to (15,d). The comparison shows that the voting algorithm is faster than its modification in all instances except the instance (15,3). We also study the effect of increasing h, which is proposed by Balla, Davila, and Rajasekaran on the modified voting algorithm. From this study, we obtained the values of the number of sequences that make the running time of modified voting algorithm less than the voting algorithm and minimum. Finally, we analyze the experimental results and give some observations according to the relations: (1) l is fixed and d is variable. (2) l is variable and d is fixed. (3) l and d are variables. (4) (l,d) is challenging.

KW - Binding site

KW - DNA motif

KW - Exact algorithm

KW - Planted (l,d)-motif

KW - Voting algorithm

UR - http://www.scopus.com/inward/record.url?scp=79952198225&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79952198225&partnerID=8YFLogxK

U2 - 10.1007/978-1-4419-5913-3_8

DO - 10.1007/978-1-4419-5913-3_8

M3 - Conference contribution

SN - 9781441959126

T3 - Advances in Experimental Medicine and Biology

SP - 65

EP - 73

BT - Advances in Computational Biology

ER -