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: | + | *[[Media:h1n1locations.zip|Location file]] containing the latitude and longitude of each geographic location, each of which could contain one or more isolates. |
| + | *[[Media:aa_sequences.zip|Sequence file]] with one row per isolate, containing metadata information including collection date and polymorphic amino acid sites. | ||
| + | *[[Media:H1N1_Concatenate_Midpoint.zip|Phylogenetic tree]] of 203 complete S-OIV sequences as determined by RAxML. | ||
| + | *[[Media:H1N1_NA248_VN_Subtree.zip|NA248 subtree]] characterized by polymorphisms at NA sites 104 and 248. | ||
| + | *[[Media:H1N1_Panmixia_Subtree.zip|Panmixia subtree] demonstrating the rapid, global spread of S-OIV. | ||
*[[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 | + | **[[Media:GenGIS_NA248_Polymorphism.zip|Python script]] used to create the above video (requires the location and sequence files above along with a [[Media:WorldMap.tif|world map]]). |
*[[Media:GenGIS_NA248_VN_Geophylogeny.swf|Stream]] video showing the geophylogeny of a subtree exhibiting polymorphism at neuraminidase site 248. | *[[Media:GenGIS_NA248_VN_Geophylogeny.swf|Stream]] video showing the geophylogeny of a subtree exhibiting polymorphism at neuraminidase site 248. | ||
| − | **[[Media:GenGIS_NA248_VN_Geophylogeny.zip|Python script]] used to create the above video (requires the | + | **[[Media:GenGIS_NA248_VN_Geophylogeny.zip|Python script]] used to create the above video (requires the location and sequence files along with one of the phylogenetic trees given above plus the [[Media:WorldMap.tif|world map]]). |
Revision as of 01:24, 26 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):
- Location file containing the latitude and longitude of each geographic location, each of which could contain one or more isolates.
- Sequence file with one row per isolate, containing metadata information including collection date and polymorphic amino acid sites.
- Phylogenetic tree of 203 complete S-OIV sequences as determined by RAxML.
- NA248 subtree characterized by polymorphisms at NA sites 104 and 248.
- [[Media:H1N1_Panmixia_Subtree.zip|Panmixia subtree] demonstrating the rapid, global spread of S-OIV.
- Stream video showing the temporal and geographic spread of neuraminidase site N248D.
- Python script used to create the above video (requires the location and sequence files above along with a world map).
- Stream video showing the geophylogeny of a subtree exhibiting polymorphism at neuraminidase site 248.
- Python script used to create the above video (requires the location and sequence files along with one of the phylogenetic trees given above plus the world map).
