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Bioinformatics Advance Access originally published online on January 29, 2004
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Bioinformatics 20(5) © Oxford University Press 2004; all rights reserved.

Java-based application framework for visualization of gene regulatory region annotations

Hao Sun and Ramana V. Davuluri *

Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 420 W 12th Avenue, TMRF 524, Columbus, OH 43210, USA

Received on December 16, 2002 ; revised on September 5, 2003 ; accepted on October 14, 2003
Advance Access Publication January 29, 2004

Motivation: The genome sequences of several organisms are either complete, or being sequenced. Each genome needs to be integrated with various types of annotations, e.g. locations of genes, promoters and other functional elements such as transcriptional regulatory elements. A robust application framework will be useful for developing web-based applications to visualize various genome annotations.

Results: We developed genome data visualization toolkit (GDVTK) as an application framework that consists of a set of data structures and core classes, using JavaTM technology. GDVTK is a sound framework for developing web-based applications to present the gene regulatory region annotations in visual form. The current version of GDVTK consists of eight packages and 38 Java classes that are portable, reusable and extensible for plugging in new data sources and models. We implemented GDVTK for visualization of promoter annotations in Mammalian Promoter Database (MPromDb), a web-based gene-regulatory information server.

Availability: GDVTK is available under GNU general public license. Source code and software documentation can be found at the URL http://bioinformatics.med.ohio-state.edu/GDVTK.

Contact: Davuluri-1{at}medctr.osu.edu

* To whom correspondence should be addressed.


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