Abstract
A weighted sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. Weighted sequences are able to summarize poorly defined short sequences, as well as the profiles of protein families and complete chromosome sequences. Thus it is of biological and theoretical significance to design powerful algorithms on weighted sequences. A common task is to identify repetitive motifs in weighted sequences, with presence probability not less than a given threshold. We define two types of repeats in weighted sequences, called the loose repeats and the strict repeats, respectively, and then attempt to locate these repeats. Using an iterative partitioning technique, we present algorithms for computing all the loose repeats and strict repeats of every length, respectively. Each solution costs O(n2)time.
Keywords: Border check array, loose repeat, partitioning, strict repeat, structural overlap, weighted sequence
Protein & Peptide Letters
Title: Loose and Strict Repeats in Weighted Sequences of Proteins
Volume: 17 Issue: 9
Author(s): Hui Zhang, Qing Guo, Jing Fan and Costas S. Iliopoulos
Affiliation:
Keywords: Border check array, loose repeat, partitioning, strict repeat, structural overlap, weighted sequence
Abstract: A weighted sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. Weighted sequences are able to summarize poorly defined short sequences, as well as the profiles of protein families and complete chromosome sequences. Thus it is of biological and theoretical significance to design powerful algorithms on weighted sequences. A common task is to identify repetitive motifs in weighted sequences, with presence probability not less than a given threshold. We define two types of repeats in weighted sequences, called the loose repeats and the strict repeats, respectively, and then attempt to locate these repeats. Using an iterative partitioning technique, we present algorithms for computing all the loose repeats and strict repeats of every length, respectively. Each solution costs O(n2)time.
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Cite this article as:
Zhang Hui, Guo Qing, Fan Jing and S. Iliopoulos Costas, Loose and Strict Repeats in Weighted Sequences of Proteins, Protein & Peptide Letters 2010; 17 (9) . https://dx.doi.org/10.2174/092986610791760324
DOI https://dx.doi.org/10.2174/092986610791760324 |
Print ISSN 0929-8665 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5305 |
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