Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Alert me when this article is cited
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 ISI Web of Science
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 (18)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Coward, E.
Right arrow Articles by Drablos, F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Coward, E.
Right arrow Articles by Drablos, F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics, Vol 14, 498-507, Copyright © 1998 by Oxford University Press

ARTICLES

Detecting periodic patterns in biological sequences

E Coward and F Drablos
Department of Mathematical Sciences, Norwegian University of Science and Technology, Norway. evindc@math.ntnu.no

MOTIVATION: The search for repeated patterns in DNA and protein sequences is important in sequence analysis. The rapid increase in available sequences, in particular from large-scale genome sequencing projects, makes it relevant to develop sensitive automatic methods for the identification of repeats. RESULTS : A new method for finding periodic patterns in biological sequences is presented. The method is based on evolutionary distance and 'phase shifts' corresponding to insertions and deletions. A given sequence is aligned to itself in a certain sense, trying to minimize a distance to periodicity. Relationships between different such periodicity measures are discussed. An iterative algorithm is used, and the running time is nearly proportional to the sequence length. The alignment produces a periodic consensus pattern. A 'phase score' is used to indicate a statistical significance of the periodicity. Three examples using both DNA and protein sequences illustrate how the method can be used to find patterns. AVAILABILITY: On request from the authors. CONTACT: evindc@mat nu.no; finn.drablos@unimed.sintef.no
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
A. Biegert and J. Soding
De novo identification of highly diverged protein repeats by probabilistic consistency
Bioinformatics, March 15, 2008; 24(6): 807 - 814.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Soding, M. Remmert, and A. Biegert
HHrep: de novo protein repeat detection and the origin of TIM barrels.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W137 - W142.
[Abstract] [Full Text] [PDF]


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.