Optimal extraction of motif patterns in 2D

Authors:
Simona E. Rombo
Affiliations:
DEIS, Università della Calabria, Via P. Bucci, 41 C Rende (CS), Italy
Venue:
Information Processing Letters
Year:
2009

Citing 6
Cited 1

Pattern discovery on character sets and real-valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm

SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
Algorithmic techniques in computational genomics

Algorithmic techniques in computational genomics
Bases of Motifs for Generating Repeated Patterns with Wild Cards

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Motif patterns in 2D

Theoretical Computer Science
Incremental discovery of the irredundant motif bases for all suffixes of a string in O(n2logn) time

Theoretical Computer Science
Optimal offline extraction of irredundant motif bases

COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics

Frequent patterns mining in multiple biological sequences

Computers in Biology and Medicine

Quantified Score

Hi-index	0.89

Visualization

Abstract

The combinatorial explosion of motif patterns occurring in 1D and 2D arrays leads to the consideration of special classes of motifs growing linearly with the size of the input array. Such motifs, called irredundant motifs, are able to succinctly represent all of the other motifs occurring in the same array within reasonable time and space bounds. In previous work irredundant motifs were extracted from 2D arrays in O(N^2log^2nloglogn) and O(N^3) time, where N is the size of the 2D input array and n is its largest dimension. In this paper, we present an algorithm to extract irredundant motifs from 2D arrays that is quadratic in the size of the input. The input is defined on a binary alphabet. It is shown that the algorithm is optimal and practically faster than the previous ones.