Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

Jeremiah J Faith1, Andrew J Olson2, Timothy S Gardner3 and Ravi Sachidanandam2*

Author Affiliations

1 Bioinformatics Program, Boston University, USA

2 Cold Spring Harbor Laboratory, USA

3 Department of Biomedical Engineering, Boston University, USA

For all author emails, please log on.

BMC Bioinformatics 2007, 8:344  doi:10.1186/1471-2105-8-344

Published: 18 September 2007

Abstract

Background

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal.

Results

lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales.

Conclusion

lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.