ALFRED
      The ALlele FREquency Database   
A resource of gene frequency data on human populations
supported by the U. S. National Science Foundation.
As a class assignment students could be asked to compare the allele frequency variation at two or three loci in a set of at least two populations from each major geographic region. There are enough populations with data on multiple loci (sites) that each student will likely have a different set of populations and polymorphisms. This will allow discussion about the ranges of variation and possible causes of the different patterns seen.

Another project would be to identify loci studied for a large number of populations and compare the global patterns of variation.

Students who can use a spreadsheet can be asked to download data on several polymorphisms, delete populations that are not typed for all of those polymorphisms and then calculate average heterozygosity for each population and Fst for each polymorphism.
Helpful tips to select populations and sites
Click on 'POPULATION' under the 'SEARCH' tab to get a list of populations by geographic region.
Separately, click on 'TABLE NUMBERS' under the 'SUMMARIES' tab. On that page under 'Graphical Overview' one can select polymorphic sites ordered by number of populations typed (#2) or populations ordered alphabetically but showing number of markers typed for each (#3), or populations ordered by number of sites typed (#4).
Any of the populations with >400 sites will have many sites in common. Most of the sites with data on more than 35 populations will have many sites in common.
In addition, the link 'Show list of sites typed for this population' on 'Population Information' page lists all the sites the population has been typed for.




A list of populations and loci can be used to search for allele frequency tables.
Helpful tips to use the keyword search function
Click on 'KEYWORD SEARCH' under the 'SEARCH' tab to get the keyword search page.
Click on the link ‘Search for frequency tables in ALFRED using gene and population names’ or scroll down to the second section of the ‘Keyword Search’ page.
Input the populations and loci (gene symbols also work) as search parameters.
An example search string would be (make sure the search parameters are separated by semi-colon) adh1b;apob;mbuti;druze;yoruba;japanese;danes


Students can compare the frequency distribution across the selected populations for the selected sites. The displayed tables can be copied and pasted into an Excel Spreadsheet for further data format manipulation and analysis.
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© 2019 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan