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Bioinformatics Advance Access published online on October 13, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti714
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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 28, 2005
Revised September 15, 2005
Accepted October 10, 2005

Applications note

Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences

Timothy R. O'Connor 1, Curtis Dyreson 2, and John J. Wyrick 1*

1 School of Molecular Biosciences, Washington State University, Pullman, WA, USA
2 School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA

* To whom correspondence should be addressed.
John J. Wyrick, E-mail: jwyrick{at}wsu.edu


  Abstract

Summary: To better understand the regulatory networks that control plant gene expression, tools are needed to systematically analyze and visualize promoter regulatory sequences in Arabidopsis thaliana. We have developed the Athena database, which contains 30,067 predicted Arabidopsis promoter sequences and consensus sequences for 105 previously characterized transcription factor (TF) binding sites. Athena provides four novel tools to facilitate the analysis of promoter sequences: a promoter visualization tool to enable the rapid inspection of key regulatory sequences in multiple promoters; a TF binding site enrichment tool to identify statistically over-represented TF sites occurring in a user-selected subset of promoters; a data mining tool to rapidly select promoter sequences containing the specified combination of TF binding sites; and a tool to display the distribution of TF binding site positions in a selected set of promoter sequences.

Availability: http://www.bioinformatics2.wsu.edu/Athena.


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