Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Ag PopGenBase Introduction

861 views

Published on

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

Published in: Education, Technology
  • Be the first to comment

Ag PopGenBase Introduction

  1. 1. Anopheles gambiae PopGenBase Tutorial vectorbase.org
  2. 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. 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. 4. [Genetic Data] Various query output format HTML format CSV format Links to chromosome images.
  5. 5. [Genetic Data] Chromosome Images
  6. 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. 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. 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. 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. 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. 11. [Documentations] Main Documentations Page Table definitions, description of allowed values and abbreviations. Formatomatic download link.

×