VectorBase: Introduction of Ag PopGenBase (Stage1) - Site Overview

1. Anopheles gambiae
PopGenBase
Tutorial
vectorbase.org

2. Main Ag PopGenBase Page
Access individual
genotype data and http://www.vectorbase.org/(TBA)
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

3. [Genetic Data]
Query page
Use left mouse button to
select an initial item and hit
HTML and csv output
Shift key + left mouse button
formats are available
Default to select an end item for
selection is choosing multiple items.
“All”
Selection
panels
Use Ctrl key
+ left mouse
button to
select multiple
Select species of interest.
items.
G for An. gambiae and R for An.
arabiensis. See additional info
about abbreviations in the
Click “Submit
“Document” section.
Query” button to
retrieve data.

4. [Genetic Data]
Various query output format
HTML format
CSV format
Links to chromosome
images.

5. [Genetic Data]
Chromosome Images

6. Formatomatic download location.
[Genetic Data]
A link is provided in Document
Formatomatic section as well.
http://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
Select input data
format and a file
for conversion.
Select an output
format and specify
output file name.

7. [Genetic Data]
Formatomatic
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.
Click ‘Convert’
button to initiate
conversion process.

8. [GoogleMaps API]
Map View
“Forms” Tab displays
chromosomal form and
molecular form distribution
Pop-up window will
of An. gambiae for this
display sample
collection site.
collection information
by year.
Click a link on the
right panels or click a
water mark to open a
pop-up window

9. [GoogleEarth]
Layer file download
Download GE layer for
genotype frequency data
summarized in pie charts
per site.
Currently IGBP Landcover
data (2004) is available as
environment descriptor.
View kmz files using
GoogleEarth. If you don’t have
GE installed, please download
from link provided here.

10. [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.
Legends for the IGBP land
cover layer is displayed on
Information window
top. However, this legend
pops up when you click
can be hidden.
the title of the layer.

11. [Documentations]
Main Documentations Page
Table definitions,
description of allowed
values and abbreviations.
Formatomatic
download link.