Difference between revisions of "Datasets"
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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): | 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): | ||
| − | *[[Media:H1N1_SOIV_Aug11.zip|H1N1 S-OIV dataset]]: metadata for 203 complete S-OIV sequences obtained from the NCBI Influenza Virus Resource on Aug. 11, 2009. | + | *[[Media:H1N1_SOIV_Aug11.zip|H1N1 S-OIV dataset]]: metadata and a phylogenetic tree for 203 complete S-OIV sequences obtained from the NCBI Influenza Virus Resource on Aug. 11, 2009. |
*[[Media:GenGIS_NA248_Polymorphism.swf|Stream]] video showing the temporal and geographic spread of neuraminidase site N248D. | *[[Media:GenGIS_NA248_Polymorphism.swf|Stream]] video showing the temporal and geographic spread of neuraminidase site N248D. | ||
**[[Media:GenGIS_NA248_Polymorphism.zip|Python script]] used to create the above video (requires the H1N1 S-OIV dataset along with a [[Media:WorldMap.tif|world map]]). | **[[Media:GenGIS_NA248_Polymorphism.zip|Python script]] used to create the above video (requires the H1N1 S-OIV dataset along with a [[Media:WorldMap.tif|world map]]). | ||
*[[Media:GenGIS_SOIV_Geophylogeny.swf|Stream]] video showing the geophylogeny of the S-OIV 2009 Influenza outbreak. | *[[Media:GenGIS_SOIV_Geophylogeny.swf|Stream]] video showing the geophylogeny of the S-OIV 2009 Influenza outbreak. | ||
**[[Media:GenGIS_SOIV_Geophylogeny.zip|Python script]] used to create the above video (requires the H1N1 S-OIV dataset along with a [[Media:WorldMap.tif|world map]]). | **[[Media:GenGIS_SOIV_Geophylogeny.zip|Python script]] used to create the above video (requires the H1N1 S-OIV dataset along with a [[Media:WorldMap.tif|world map]]). | ||
Revision as of 18:05, 25 August 2009
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 and a phylogenetic tree 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.
- Python script used to create the above video (requires the H1N1 S-OIV dataset along with a world map).
- Stream video showing the geophylogeny of the S-OIV 2009 Influenza outbreak.
- Python script used to create the above video (requires the H1N1 S-OIV dataset along with a world map).
