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


CONCLUSIONS
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.
Faith
Jeremiah J
JJ
Bioinformatics Program, Boston University, USA. faith@bu.edu
Olson
Andrew J
AJ
Gardner
Timothy S
TS
Sachidanandam
Ravi
R
D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003628:Database Management Systems; D023061:Gene Order; D016680:Genome, Bacterial; D016681:Genome, Fungal; D015894:Genome, Human; D023281:Genomics / Q000379:methods* / Q000458:organization & administration*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D026801:Synteny; D014584:User-Computer Interface