GenGIS: A geospatial information system for genomic data
- Donovan H. Parks1,
- Michael Porter1,
- Sylvia Churcher1,
- Suwen Wang1,
- Christian Blouin1,
- Jacqueline Whalley2,
- Stephen Brooks1 and
- Robert Beiko1,3
- * Corresponding author; email: beiko{at}cs.dal.ca
Abstract
The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis which can integrate digital maps, ecological data, and large genetic, genomic or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets.
Footnotes
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- Received May 3, 2009.
- Accepted July 16, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
