Discovering well-ordered folding patterns in nucleotide sequences

Statistical Inference for Well-ordered Structures in Nucleotide Sequences

Distinct, local structures are frequently correlated with functional RNA elements involved in post-transcriptional regulation of gene expression. Discovery of microRNAs (miRNAs) suggests that there are a large class of small non-coding RNAs in eukaryotic genomes. These miRNAs have the potential to form distinct fold-back stem-loop structures. The prediction of those well-ordered folding sequenc...

Discovering Patterns in Sequences of Events

Dynamics of Charge Transfer in Ordered and Chaotic Nucleotide Sequences

Charge transfer is considered in systems composed of a donor, an acceptor and bridge sites of (AT) nucleotide pairs. For a bridge consisting of 180 (AT) pairs, three cases are dealt with: a uniform case, when all the nucleotides in each strand are identical; an ordered case, when nucleotides in each DNA strand are arranged in an orderly fashion; a chaotic case, when (AT) and (TA) pairs are arra...

Discovering Unordered and Ordered Phrase Association Patterns for Text Mining

This paper considers the problem of nding all frequent phrase association patterns in a large collection of unstructured texts, where a phrase association pattern is a set of consecutive sequences of arbitrary number of keywords which appear together in a document. For the ordered and the unordered versions of phrase association patterns, we present eecient algorithms, called Levelwise-Scan, ba...

Discovering Partial Periodic Patterns in Discrete Data Sequences

The problem of partial periodic pattern mining in a discrete data sequence is to find subsequences that appear periodically and frequently in the data sequence. Two essential subproblems are the efficient mining of frequent patterns and the automatic discovery of periods that correspond to these patterns. Previous methods for this problem in event sequence databases assume that the periods are ...