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

Hao Sun, Ramana V. Davuluri*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)727-734
Number of pages8
JournalBioinformatics
Volume20
Issue number5
DOIs
StatePublished - Mar 22 2004

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint Dive into the research topics of 'Java-based application framework for visualization of gene regulatory region annotations'. Together they form a unique fingerprint.

Cite this