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Bioinformatics Advance Access published online on November 17, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti787
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 27, 2005
Revised September 20, 2005
Accepted November 15, 2005

Applications note

Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series

Jo Criel 1 and Elena Tsiporkova 2 *

1 Devgen N.V., Science IT, Technologiepark 30, B-9052 Gent, Belgium
2 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052, Gent, Belgium

* To whom correspondence should be addressed.
Elena Tsiporkova, E-mail: eltsi{at}psb.ugent.be


  Abstract

Summary: An application tool for alignment, template matching and visualization of gene expression time series is presented. The core algorithm is based on dynamic time warping techniques used in the speech recognition field. These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases.

Availability: The Java program, examples and a tutorial are available at http://www.psb.ugent.be/cbd/papers/gentxwarper/.


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