## Space and time efficient algorithms for planted motif search (2006)

Venue: | Proc. 6th International Conference on Computational Science (ICCS 2006)/ 2nd International Workshop on Bioinformatics Research and Applications (IWBRA 2006) LNCS 3992 |

Citations: | 8 - 4 self |

### BibTeX

@INPROCEEDINGS{Davila06spaceand,

author = {Jaime Davila and Sudha Balla and Sanguthevar Rajasekaran},

title = {Space and time efficient algorithms for planted motif search},

booktitle = {Proc. 6th International Conference on Computational Science (ICCS 2006)/ 2nd International Workshop on Bioinformatics Research and Applications (IWBRA 2006) LNCS 3992},

year = {2006},

pages = {822--829}

}

### OpenURL

### Abstract

Abstract. We consider the (l, d) Planted Motif Search Problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose the algorithms PMSi and PMSP which are based on ideas considered in PMS1 [10]. These algorithms are exact, make use of less space than the known exact algorithms such as PMS and are able to tackle instances with large values of d. In particular algorithm PMSP is able to solve the challenge instance (17, 6), which has not reported solved before in the literature. 1

### Citations

226 | Finding Motifs Using Random Projections
- Bulher, Tompa
- 2002
(Show Context)
Citation Context ... in the polynomial complexity of the PTAS makes it of little practical use. Numerous algorithms have been implemented in order to solve instances of this problem. Among them we have Random Projection =-=[2]-=-, MITRA [4], Winnower [8], Pattern Branching [9], Hybrid Sample and Pattern Driven Approaches [12], PMS1 [10], CENSUS [5] and Voting [3]. ⋆ This research was supported in part by the NSF Grant ITR-032... |

207 | Combinatorial approaches to finding subtle signals in DNA sequences
- Pevzner, Sze
- 2000
(Show Context)
Citation Context ...xity of the PTAS makes it of little practical use. Numerous algorithms have been implemented in order to solve instances of this problem. Among them we have Random Projection [2], MITRA [4], Winnower =-=[8]-=-, Pattern Branching [9], Hybrid Sample and Pattern Driven Approaches [12], PMS1 [10], CENSUS [5] and Voting [3]. ⋆ This research was supported in part by the NSF Grant ITR-0326155.sOut of these algori... |

79 | Finding composite regulatory patterns in DNA sequences
- Eskin, Pevzner
- 2002
(Show Context)
Citation Context ...ynomial complexity of the PTAS makes it of little practical use. Numerous algorithms have been implemented in order to solve instances of this problem. Among them we have Random Projection [2], MITRA =-=[4]-=-, Winnower [8], Pattern Branching [9], Hybrid Sample and Pattern Driven Approaches [12], PMS1 [10], CENSUS [5] and Voting [3]. ⋆ This research was supported in part by the NSF Grant ITR-0326155.sOut o... |

58 | On the closest string and substring problems
- Li, Ma, et al.
(Show Context)
Citation Context .... dH(x, xi) = d for i = 1, . . . , n. This problem is known to be NP-complete [6] and a PTAS exists for variants of the problem known as the Common Approximate Substring and Common Approximate String =-=[7]-=-, [1]. However the high degree in the polynomial complexity of the PTAS makes it of little practical use. Numerous algorithms have been implemented in order to solve instances of this problem. Among t... |

33 | Finding subtle motifs by branching from sample strings
- Price, Ramabhadran, et al.
- 2003
(Show Context)
Citation Context ...it of little practical use. Numerous algorithms have been implemented in order to solve instances of this problem. Among them we have Random Projection [2], MITRA [4], Winnower [8], Pattern Branching =-=[9]-=-, Hybrid Sample and Pattern Driven Approaches [12], PMS1 [10], CENSUS [5] and Voting [3]. ⋆ This research was supported in part by the NSF Grant ITR-0326155.sOut of these algorithms, CENSUS, MITRA, PM... |

29 | 2005b) Voting Algorithm for Discovering Long Motifs
- Chin, Leung
(Show Context)
Citation Context ...instances of this problem. Among them we have Random Projection [2], MITRA [4], Winnower [8], Pattern Branching [9], Hybrid Sample and Pattern Driven Approaches [12], PMS1 [10], CENSUS [5] and Voting =-=[3]-=-. ⋆ This research was supported in part by the NSF Grant ITR-0326155.sOut of these algorithms, CENSUS, MITRA, PMS1 and Voting are in the exact category. The last two algorithms are able to work in rea... |

16 | On the complexity of finding common approximate substrings. Theoret
- Evans, Smith, et al.
- 2003
(Show Context)
Citation Context ...) motif search problem as that of finding a string x with |x| = l such that si has an l-mer xi with We will call x a motif. dH(x, xi) = d for i = 1, . . . , n. This problem is known to be NP-complete =-=[6]-=- and a PTAS exists for variants of the problem known as the Common Approximate Substring and Common Approximate String [7], [1]. However the high degree in the polynomial complexity of the PTAS makes ... |

11 | Exact algorithms for planted motif problems
- Rajasekaran, Balla, et al.
(Show Context)
Citation Context ...rch Problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose the algorithms PMSi and PMSP which are based on ideas considered in PMS1 =-=[10]-=-. These algorithms are exact, make use of less space than the known exact algorithms such as PMS and are able to tackle instances with large values of d. In particular algorithm PMSP is able to solve ... |

9 | Toward optimal motif enumeration
- Evans, Smith
- 2003
(Show Context)
Citation Context ...order to solve instances of this problem. Among them we have Random Projection [2], MITRA [4], Winnower [8], Pattern Branching [9], Hybrid Sample and Pattern Driven Approaches [12], PMS1 [10], CENSUS =-=[5]-=- and Voting [3]. ⋆ This research was supported in part by the NSF Grant ITR-0326155.sOut of these algorithms, CENSUS, MITRA, PMS1 and Voting are in the exact category. The last two algorithms are able... |

8 |
Integrating sample-driven and pattern-driven approaches in motif finding
- Sze, Lu, et al.
- 2004
(Show Context)
Citation Context ...ave been implemented in order to solve instances of this problem. Among them we have Random Projection [2], MITRA [4], Winnower [8], Pattern Branching [9], Hybrid Sample and Pattern Driven Approaches =-=[12]-=-, PMS1 [10], CENSUS [5] and Voting [3]. ⋆ This research was supported in part by the NSF Grant ITR-0326155.sOut of these algorithms, CENSUS, MITRA, PMS1 and Voting are in the exact category. The last ... |

2 |
S.: Approximation Algorithms for the Primer Selection, Planted Motif Search, and Related Problems
- Balla, Davila, et al.
- 2006
(Show Context)
Citation Context ...x, xi) = d for i = 1, . . . , n. This problem is known to be NP-complete [6] and a PTAS exists for variants of the problem known as the Common Approximate Substring and Common Approximate String [7], =-=[1]-=-. However the high degree in the polynomial complexity of the PTAS makes it of little practical use. Numerous algorithms have been implemented in order to solve instances of this problem. Among them w... |

2 |
Motif Search Algorithms in Handbook of Computational Molecular Biology CRC Press; 2006. doi:10.1186/1756-0500-4-54 Cite this article as: Rajasekaran and Dinh: A speedup technique for (l, d)motif finding algorithms. BMC Research Notes 2011 4:54. Submit you
- Rajasekaran
(Show Context)
Citation Context ...0 and n = 20. In [2] the notion of a challenging instance was defined, as one where if the strings are selected at random, the expected number of (l, d) motifs is greater than 1. We have that (9, 2), =-=(11, 3)-=-, (13, 4), (15, 5) and (17, 6) are challenging instances. PMS1 is able to solve (9, 2),(11, 3) and (13, 4) in less than a couple of minutes, and Voting is able to solve these instances and (15, 5) –th... |