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Nucleic Acids Research 2005 33(15):e134; doi:10.1093/nar/gni135
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Published online 1 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses

David S. H. Chew1,*, Kwok Pui Choi1,2 and Ming-Ying Leung3,4

1Department of Mathematics, National University of Singapore Singapore 2Department of Statistics and Applied Probability, National University of Singapore Singapore 3Bioinformatics Program, University of Texas at El Paso El Paso, Texas 79968, USA 4Department of Mathematical Sciences, University of Texas at El Paso El Paso, Texas 79968, USA

*To whom correspondence should be addressed. Tel: +65 6847 1653; Fax: +65 6779 5452; Email: matchewd{at}nus.edu.sg

Received May 30, 2005. Revised June 27, 2005. Accepted August 15, 2005.

Many empirical studies show that there are unusual clusters of palindromes, closely spaced direct and inverted repeats around the replication origins of herpesviruses. In this paper, we introduce two new scoring schemes to quantify the spatial abundance of palindromes in a genomic sequence. Based on these scoring schemes, a computational method to predict the locations of replication origins is developed. When our predictions are compared with 39 known or annotated replication origins in 19 herpesviruses, close to 80% of the replication origins are located within 2% of the genome length. A list of predicted locations of replication origins in all the known herpesviruses with complete genome sequences is reported.


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