Lightweight Genome Viewer: portable software for browsing genomics data in its chromosomal context

Faith, Jeremiah J.; Olson, Andrew J.; Gardner, Timothy S.; Sachidanandam, Ravi

doi:10.1186/1471-2105-8-344

Title: Lightweight Genome Viewer: portable software for browsing genomics data in its chromosomal context

Journal Article · Tue Sep 18 00:00:00 EDT 2007 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-8-344· OSTI ID:1626343

Faith, Jeremiah J. ^[1]; Olson, Andrew J. ^[2]; Gardner, Timothy S. ^[3]; Sachidanandam, Ravi ^[2]

Boston Univ., MA (United States). Bioinformatics Program
Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
Boston Univ., MA (United States). Dept. of Biomedical Engineering

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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Research Organization:: Boston Univ., MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-04ER63803

OSTI ID:: 1626343

Journal Information:: BMC Bioinformatics, Vol. 8, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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