ag popgenbase introduction
DESCRIPTION
VectorBase: Introduction of Ag PopGenBase (Stage1) - Site OverviewTRANSCRIPT
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Anopheles gambiae
PopGenBase
Tutorial
vectorbase.org
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http://www.vectorbase.org/(TBA)
Main Ag PopGenBase Page
Access individual
genotype data and
chromosome images.
See distribution of
genetic polymorphism
on maps in real time.
Download pre-
generated GoogleEarth
layers for visualizing
genotype frequency and
environment.
PopGenBase Tutorial
and other documents for
data organizations and
naming conventions
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[Genetic Data]
Query page
Selection
panels
Use Ctrl key
+ left mouse
button to
select multiple
items.
Default
selection is
“All”
Select species of interest.
G for An. gambiae and R for An.
arabiensis. See additional info
about abbreviations in the
“Document” section.
HTML and csv output
formats are available
Use left mouse button to
select an initial item and hit
Shift key + left mouse button
to select an end item for
choosing multiple items.
Click “Submit
Query” button to
retrieve data.
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[Genetic Data]
Various query output format
HTML format
CSV formatLinks to chromosome
images.
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[Genetic Data]
Chromosome Images
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[Genetic Data]
Formatomatichttp://taylor0.biology.ucla.edu/~manoukis/Pub_programs/Formatomatic/N. C. Manoukis (2007) Formatomatic: a program for converting diploid allelic data between common formats for population genetic analysis
Formatomatic download location.A link is provided in Document
section as well.
Select input data format and a file
for conversion.
Select an output format and specify
output file name.
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[Genetic Data]
Formatomatic
Click ‘Convert’button to initiate
conversion process.
If conversion fails, error messages gives
you a clue on how to fix the problem. In this case, output file name was not
specified, which generated an error.
Message when a conversion was
successful.
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[GoogleMaps API]
Map View
Click a link on the
right panels or click a water mark to open a
pop-up window
Pop-up window will
display sample collection information
by year.
“Forms” Tab displays chromosomal form and
molecular form distribution
of An. gambiae for this collection site.
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[GoogleEarth]
Layer file downloadDownload GE layer for
genotype frequency data summarized in pie charts
per site.
Currently IGBP Landcoverdata (2004) is available as
environment descriptor.
View kmz files using
GoogleEarth. If you don’t have GE installed, please download
from link provided here.
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[GoogleEarth]
Layer View on GoogleEarth
Square with a green checkmark indicates a particular layer is on
view. For example, the “Species” and “Forms”layer is on view but the
“inversion 2La” layer is hidden from view.
Information window pops up when you click
the title of the layer.
Legends for the IGBP land
cover layer is displayed on top. However, this legend
can be hidden.
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[Documentations]
Main Documentations Page
Formatomaticdownload link.
Table definitions, description of allowed
values and abbreviations.