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. 2007 Sep 18:8:344.
doi: 10.1186/1471-2105-8-344.

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

Jeremiah J Faith  1 , Andrew J Olson, Timothy S Gardner, Ravi Sachidanandam
Affiliations

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

Jeremiah J Faith et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
A screenshot of the results from a siRNA design visualization demonstrates how lwgv represents sequence features on tracks. In this case, the features of interest are the coding sequence (CDS) of the gene being used for RNAi and the location of the designed oligos on that CDS. lwgv also allows the sequence itself to be displayed and colored according to the information in the track.
Figure 2
Figure 2
Example of the trackCorrelate function to help visualize splice variants. RefSeq and other mRNAs from the human gene BRCA1 are shown aligned to the genome (a) and after compressing introns (b). After compression, it is much easier to see the different isoforms and, for example, discover that mRNAs BC072418.1 and AF005068.1 are not represented among the RefSeqs.
Figure 3
Figure 3
lwgv is used with the Many Microbe Microarrays Database to allow users to dynamically display expression changes in their chromosomal context. In this example, significant expression changes between E. coli cells grown in rich media and E. coli cells grown in rich media with norfloxacin antibiotic are shown with lwgv. In this chromosomal context, it is immediately clear that several large regions of the genome have significantly changed expression levels between these two conditions. For example, over 28 consecutive genes and intergenic regions related to flagella have a significant fold change (track grp fold). These significantly changed genes are displayed on track sig fold.
See this image and copyright information in PMC

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