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Nucleic Acids Research 2005 33(2):e12; doi:10.1093/nar/gni003
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Published online 19 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 2 © Oxford University Press 2005; 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 permissions, please contact journals.permissions{at}oupjournals.org.

Methods Online

A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes

Jongmin Nam*, Kerstin Kaufmann1, Günter Theißen1 and Masatoshi Nei

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University University Park, PA 16802, USA 1 Lehrstuhl für Genetik, Friedrich-Schiller-Universität Jena Philosophenweg 12, D-07743, Jena, Germany

*To whom correspondence should be addressed. Tel: +1 814 865 2796; Fax: +1 814 863 7336; Email: JYN101{at}PSU.EDU

Received September 20, 2004. Revised November 29, 2004. Accepted December 9, 2004.

A simple statistical method for predicting the functional differentiation of duplicate genes was developed. This method is based on the premise that the extent of functional differentiation between duplicate genes is reflected in the difference in evolutionary rate because the functional change of genes is often caused by relaxation or intensification of functional constraints. With this idea in mind, we developed a window analysis of protein sequences to identify the protein regions in which the significant rate difference exists. We applied this method to MIKC-type MADS-box proteins that control flower development in plants. We examined 23 pairs of sequences of floral MADS-box proteins from petunia and found that the rate differences for 14 pairs are significant. The significant rate differences were observed mostly in the K domain, which is important for dimerization between MADS-box proteins. These results indicate that our statistical method may be useful for predicting protein regions that are likely to be functionally differentiated. These regions may be chosen for further experimental studies.


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