Volume 4, Issue 5, October 2011, Pages 1032 - 1041
A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences
- Caiyan Jia, Ruqian Lu, Lusheng Chen
- Corresponding Author
- Caiyan Jia
Available Online 6 December 2011.
- https://doi.org/10.2991/ijcis.2011.4.5.26How to use a DOI?
- Motif, frequent pattern, Apriori, downward closure property.
- Identification and characterization of gene regulatory binding motifs is one of the fundamental tasks toward systematically understanding the molecular mechanisms of transcriptional regulation. Recently, the problem has been abstracted as the challenge planted (l,d)-motif problem. Previous studies have developed numerous methods to solve the problem. But most of them need to specify the length l of a planted motif in advance and use depth first search strategy. In this study, we present an exact and efficient algorithm, called Apriori-Motif, without given the length l of a planted motif a priori. And a breadth first search strategy is used to prune search space quickly by the downward closure property utilized in Apriori, which is a classical algorithm for frequent pattern mining. Empirical study shows that Apriori-Motif is better than some existing methods.
- Open Access
- This is an open access article distributed under the CC BY-NC license.
Cite this article
TY - JOUR AU - Caiyan Jia AU - Ruqian Lu AU - Lusheng Chen PY - 2011 DA - 2011/12 TI - A Frequent Pattern Mining Method for Finding Planted Motifs of Unknown Length in DNA Sequences JO - International Journal of Computational Intelligence Systems SP - 1032 EP - 1041 VL - 4 IS - 5 SN - 1875-6883 UR - https://doi.org/10.2991/ijcis.2011.4.5.26 DO - https://doi.org/10.2991/ijcis.2011.4.5.26 ID - Jia2011 ER -