Introduction

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.

Publications

  1. D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements.
    Cite this
    Laimer J, Zuzan CJ, Ehrenberger T, Freudenberger M, Gschwandtner S, Lebherz C, Lackner P, 2013-01-01 - BMC bioinformatics

Credits

  1. Josef Laimer
    Developer

    Department of Molecular Biology, University of Salzburg, Austria

  2. Clemens J Zuzan
    Developer

  3. Tobias Ehrenberger
    Developer

  4. Monika Freudenberger
    Developer

  5. Simone Gschwandtner
    Developer

  6. Carina Lebherz
    Developer

  7. Peter Lackner
    Investigator

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Summary
AccessionBT006571
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByPeter Lackner