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

Hao Sun; Ramana V Davuluri

doi:10.1093/bioinformatics/btg476

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

Hao Sun·Ramana V Davuluri

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Abstract

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 Java 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.

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Computer Graphics Database Management Systems Databases, Genetic Documentation Hypermedia Information Storage and Retrieval Internet Programming Languages Regulatory Sequences, Nucleic Acid Software User-Computer Interface Evaluation Study Journal Article

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Hao Sun, Ramana V Davuluri. 2004-01-29. Java-based application framework for visualization of gene regulatory region annotations.. https://doi.org/10.1093/bioinformatics%2Fbtg476

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