Skip Navigation


Bioinformatics Advance Access originally published online on January 19, 2007
Bioinformatics 2007 23(6):694-700; doi:10.1093/bioinformatics/btl674
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
23/6/694    most recent
btl674v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (2)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Brodzik, A. K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Brodzik, A. K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem

Andrzej K. Brodzik

The MITRE Corporation, Bedford MA 01730


  Abstract

Motivation: One of the main tasks of DNA sequence analysis is identification of repetitive patterns. DNA symbol repetitions play a key role in a number of applications, including prediction of gene and exon locations, identification of diseases, reconstruction of human evolutionary history and DNA forensics.

Results: A new approach towards identification of tandem repeats in DNA sequences is proposed. The approach is a refinement of previously considered method, based on the complex periodicity transform. The refinement is obtained, among others, by mapping of DNA symbols to pure quaternions. This mapping results in an enhanced, symbol-balanced sensitivity of the transform to DNA patterns, and an unambiguous threshold selection criterion. Computational efficiency of the transform is further improved, and coupling of the computation with the period value is removed, thereby facilitating parallel implementation of the algorithm. Additionally, a post-processing stage is inserted into the algorithm, enabling unambiguous display of results in a convenient graphical format. Comparison of the quaternionic periodicity transform with two well-known pattern detection techniques shows that the new approach is competitive with these two techniques in detection of exact and approximate repeats.

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on August 25, 2006; revised on December 10, 2006; accepted on January 3, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.