Abstract
BackgroundLightweight 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.Resultslwgv 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.Conclusionlwgv 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.
Highlights
Lightweight genome viewer is a web-based tool for visualization of sequence annotations in their chromosomal context
There has been a push towards feature-rich species-generic genome browsers that can be reused for new genomes
We present a new application of lwgv to dynamically visualize changes in gene expression along a genome using any combination of the over 500 prokaryotic microarrays available in the Many Microbe Microarrays Database (M3D). lwgv is an ideal tool for the presentation of dynamic analyses and sequence annotations without resorting to the creation and maintenance of a large database and software infrastructure
Summary
Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. These software systems are web-based and present an image with "tracks" of information that describe the underlying genome sequence. The requirement of a relational database complicates the genome browsers' applicability in dynamic contexts that change frequently.
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