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Open Access Software

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements

Josef Laimer12, Clemens J Zuzan1, Tobias Ehrenberger2, Monika Freudenberger2, Simone Gschwandtner2, Carina Lebherz2 and Peter Lackner1*

Author Affiliations

1 Department of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria

2 Upper Austria University of Applied Sciences, Softwarepark 11, 4232 Hagenberg, Austria

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BMC Bioinformatics 2013, 14:140  doi:10.1186/1471-2105-14-140

Published: 24 April 2013

Abstract

Background

The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms.

Results

We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set.

Conclusions

D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight webcite.