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Instructions

Introduction

MLST-Maps
    eBURST
    Trees

Database Query
    Results
    Maps

    eBURST
    Trees
    Download Data

Locus Query
    Sinlgle

    Multiple
    Batch

ST & Profile Query
    Sinlgle
    Batch
    ST Query

eBURST
    User data
    Geographic

Downloading Data

Organism Specific

Submitting Data
    alleles
    Sequence Types
    Isolate data
    Next-gen data

 

Policy Document

MLST-Maps

We have integrated Google Maps within our MLST websites allowing you to explore the geographic distribution of the isolates in the database and the distribution of individual STs. Furthermore, you can compare STs from different countries using either 'geographic eBURST' or trees.

On clicking the MLST-Maps link on a database you are initially presented with a Google map with placemarks (pins on the map) indicating the country of origin of isolates whose details have been deposited in the database. Placemarks are coloured according to the % of isolates in the database submitted from that location. For almost all MLST websites, only the country of origin of isolates in the database is available but more detailed mapping is available for MLST sites where detailed geographic data have been deposited (e.g., Leptospira.from Thailand) and we encourage those that develope new MLST sites to include more detailed information on the geographic source of isolates (ideally using GPS co-ordinates).

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Each placemark on the map (located at the centroid of each country) indicates that isolates from that location are available in the database. Clicking on any placemark produces an 'Info Window' indicating the number of isolates from that location in the database and a link to 'Click to view STs' (as above).

On clicking the link within an Info Window, the map zooms to that country and summary data on the isolates from the country, and a number of TABS related to these country data, are shown below the map, as in the following screenshot.

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The country you have chosen is indicated below the map to the left (in this example, Brazil), and the small globe icon on the right below the map allows you to 'click to return' to the world view at any point.

 

Four TABS are available and provide isolate data and display tools:

1) Sequence Type Summary

The 'Sequence Type Summary' TAB provides a table with details of the isolates in the MLST database from the selected country - Brazil in the above map.

The first two columns show the number of isolates of each ST from Brazil.


Columns 3-9 show the alleles at each of the seven loci for each ST (i.e. the allelic profile).


The penultimate column indicates whether the ST has been found in any other countries (the first number) followed, in parentheses, by the total number of isolates of the ST in the database from the other countries.


The final column contains a 'click to view on map' link that will show the global distribution of a particular ST, as in the following screenshot, which shows the global distribution of the most common Brazilian strain - ST66.

The new map has a placemark for every country from which isolates of the selected ST are present in the database. The numbers within each placemark indicate the number of isolates of that ST from each country.

At the top of the map, a grey box indicates which ST you have chosen and includes a link to return the initial map view for the country you chose.

 

2) Epidemiological data

 

The 'Epidemiological data' TAB shows further details of the isolates in the database from the selected country, as below.

Further details on each isolate can be obtained by clicking on the id number of each isolate or .....

 

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The next section describes the use of eBURST to compare the STs from the selected country with those from another country or countries.

 

 

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