Datasets

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The following datasets were analyzed in GenGIS: A geospatial information system for genomic data (Parks et al., Genome Res., 2009):

  • GOS dataset: taxonomic diversity of Atlanatic seaboard sites from the Global Ocean Sampling expedition.
  • HIV-1 dataset: geographic distribution of non-recombinant HIV-1 subtypes in Africa
  • ISEA mtDNA dataset: phylogenetic distribution of mtDNA haplogroup E, using hypervariable segment I (HVS-I) sequences from Southeast Asia.


The following datasets were analyzed in Tracking the evolution and geographic spread of Influenza A (Parks et al., PLoS Currents: Influenza, submitted Aug. 25, 2009):

  • H1N1 S-OIV dataset: metadata for 203 complete S-OIV sequences obtained from the NCBI Influenza Virus Resource on Aug. 11, 2009.
  • Stream video showing the temporal and geographic spread of neuraminidase site N248D as determined from sequences published at the NCBI Influenza Virus Resource as of August 11, 2009.
  • Python script: python script used to create the above video (requires the H1N1 S-OIV dataset) along with a Sample world map.