GenGIS: A Geospatial Information System for Genomic Data

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aut.publication.placeHalifax, Nova Scotia, Canadaen_NZ
aut.relation.softwareversionv1.07en_NZ
dark.contributor.authorBieko, RGen_NZ
dark.contributor.authorStephen, Ben_NZ
dark.contributor.authorBlouin, Cen_NZ
dark.contributor.authorParks, Den_NZ
dark.contributor.authorPorter, Men_NZ
dark.contributor.authorWang, Sen_NZ
dark.contributor.authorChurcher, Sen_NZ
dc.date.accessioned2023-01-25T01:29:22Z
dc.date.available2023-01-25T01:29:22Z
dc.date.copyright2009en_NZ
dc.date.issued2009en_NZ
dc.description.abstractThe 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 that 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.
dc.identifier.citationGenome Research, 19(10), 1896–1904. https://doi.org/10.1101/gr.095612.109
dc.identifier.doi10.1101/gr.095612.109en_NZ
dc.identifier.urihttps://hdl.handle.net/10292/15840
dc.publisherCold Spring Harbor Laboratory Pressen_NZ
dc.relation.urihttps://genome.cshlp.org/content/19/10/1896en_NZ
dc.rights.accessrightsOpenAccessen_NZ
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.titleGenGIS: A Geospatial Information System for Genomic Dataen_NZ
dc.typeSoftware
pubs.elements-id461150
pubs.organisational-data/AUT
pubs.organisational-data/AUT/Faculty of Design & Creative Technologies
pubs.organisational-data/AUT/Faculty of Design & Creative Technologies/School of Engineering, Computer & Mathematical Sciences
pubs.organisational-data/AUT/PBRF
pubs.organisational-data/AUT/PBRF/PBRF Design and Creative Technologies
pubs.organisational-data/AUT/PBRF/PBRF Design and Creative Technologies/PBRF ECMS
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