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Bioinformatics. 2013 Sep 1;29(17):2195-6. doi: 10.1093/bioinformatics/btt354. Epub 2013 Jun 19.

GPViz: dynamic visualization of genomic regions and variants affecting protein domains.

Author information

1
Biocenter, Division of Bioinformatics, Innsbruck Medical University and Oncotyrol Center for Personalized Cancer Medicine GmbH, 6020 Innsbruck, Austria.

Abstract

GPViz is a versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User-defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively. Various gene filter options are provided to enable an intersection of variants, genomic regions and affected protein features. Finally, by using GPViz, we identified differentially expressed exons, which could indicate alternative splicing events, and found somatic variants in different cancer types affecting metabolic proteins. GPViz is freely available at http://icbi.at/gpviz (released under GNU general public license), is based on Java 7 and can be used as a stand-alone or Web Start application.

AVAILABILITY:

http://icbi.at/gpviz

PMID:
23782613
DOI:
10.1093/bioinformatics/btt354
[Indexed for MEDLINE]

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