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Nucleic Acids Research 2006 34(Web Server issue):W482-W485; doi:10.1093/nar/gkl162
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© The Author 2006. 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@oxfordjournals.org

Article

BTW: a web server for Boltzmann time warping of gene expression time series

F. Ferrè and P. Clote*

Department of Biology, Boston College Chestnut Hill, MA USA

*To whom correspondence should be addressed at Departments of Biology and Computer Science (courtesy appointment), Boston College, Chestnut Hill, MA USA. Tel: +1 617 552 1332; Fax: +1 617 552 2011; Email: clote{at}bc.edu

Received March 8, 2006. Accepted March 20, 2006.

Dynamic time warping (DTW) is a well-known quadratic time algorithm to determine the smallest distance and optimal alignment between two numerical sequences, possibly of different length. Originally developed for speech recognition, this method has been used in data mining, medicine and bioinformatics. For gene expression time series data, time warping distance is arguably a more flexible tool to determine genes having similar temporal expression, hence possibly related biological function, than either Euclidean distance or correlation coefficient—especially since time warping accommodates sequences of different length. The BTW web server allows a user to upload two tab-separated text files A,B of gene expression data, each possibly having a different number of time intervals of different durations. BTW then computes time warping distance between each gene of A with each gene of B, using a recently developed symmetric algorithm which additionally computes the Boltzmann partition function and outputs Boltzmann pair probabilities. The Boltzmann pair probabilities, not available with any other existent software, suggest possible biological significance of certain positions in an optimal time warping alignment. Availability: http://bioinformatics.bc.edu/clotelab/BTW/.


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F. Ferre, Y. Ponty, W. A. Lorenz, and P. Clote
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