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Title: Nonrandom clusters of palindromes in herpesvirus genomes
Authors: Leung, M.-Y.
Kwok, P.C. 
Xia, A.
Chen, L.H.Y. 
Keywords: DNA palindromes
Poisson process approximation
Replication origins
Scan statistics
Wasserstein distance
Issue Date: 2005
Citation: Leung, M.-Y., Kwok, P.C., Xia, A., Chen, L.H.Y. (2005). Nonrandom clusters of palindromes in herpesvirus genomes. Journal of Computational Biology 12 (3) : 331-354. ScholarBank@NUS Repository.
Abstract: Palindromes are symmetrical words of DNA in the sense that they read exactly the same as their reverse complementary sequences. Representing the occurrences of palindromes in a DNA molecule as points on the unit interval, the scan statistics can be used to identify regions of unusually high concentration of palindromes. These regions have been associated with the replication origins on a few herpesviruses in previous studies. However, the use of scan statistics requires the assumption that the points representing the palindromes are independently and uniformly distributed on the unit interval. In this paper, we provide a mathematical basis for this assumption by showing that in randomly generated DNA sequences, the occurrences of palindromes can be approximated by a Poisson process. An easily computable upper bound on the Wasserstein distance between the palindrome process and the Poisson process is obtained. This bound is then used as a guide to choose an optimal palindrome length in the analysis of a collection of 16 herpesvirus genomes. Regions harboring significant palindrome clusters are identified and compared to known locations of replication origins. This analysis brings out a few interesting extensions of the scan statistics that can help formulate an algorithm for more accurate prediction of replication origins. © Mary Ann Liebert, Inc.
Source Title: Journal of Computational Biology
ISSN: 10665277
DOI: 10.1089/cmb.2005.12.331
Appears in Collections:Staff Publications

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