- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Data Supplement
-
All Versions of this Article:
genetics.106.068874v1
176/2/1035 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Boni, M. F.
- Articles by Feldman, M. W.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Boni, M. F.
- Articles by Feldman, M. W.
Originally published as Genetics Published Articles Ahead of Print on April 3, 2007.
Genetics, Vol. 176, 1035-1047, June 2007, Copyright © 2007
doi:10.1534/genetics.106.068874
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets
Maciej F. Boni*,
,1,
David Posada
and
Marcus W. Feldman
* Stanford Genome Technology Center, Palo Alto, California 94304, Department of Biological Sciences, Stanford University, Stanford, California 94305 and Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
1 Corresponding author: Stanford Genome Technology Center, 855 S. California Ave., Palo Alto, CA 94304.
E-mail: maciek{at}charles.stanford.edu
Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic 
m,n,b. We present a method for rapidly calculating the distribution of m,n,b and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
This article has been cited by other articles:
 |
|
 |
|
  F. M. Codoner and S. F. Elena The promiscuous evolutionary history of the family Bromoviridae J. Gen. Virol., July 1, 2008; 89(7): 1739 - 1747. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. F. Boni, Y. Zhou, J. K. Taubenberger, and E. C. Holmes Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus J. Virol., May 15, 2008; 82(10): 4807 - 4811. [Abstract] [Full Text] [PDF]
|
|