The ALlele FREquency Database    A resource of gene frequency data on human populations supported by the U. S. National Science Foundation.

The simplest search involves searching for frequency records. The resulting output is either a table or semicolon delimited text. The table is easier to read, while the semicolon delimited text can be imported into a spreadsheet. To perform a search, enter the desired search specifications into the appropriate fields. For instance, if you wish to find all frequency records for chromosome 4 typed on the Finns and Danes, you would choose chromosome 4 from the Chromosome pull-down list, and enter "Finns,Danes" in the field "Population". If you desire semicolon delimited text, click in the box to the left of "Semicolon Delimited Output".

• Search for frequency records by locus

  You may want to perform a search, but not know the exact name of the locus you are interested in. In that case, you can go to the main page to search for frequencies and click on Show all just to the right of the Locus field. A pulldown list of chromosomes will appear. If you know the chromosome the locus you are interested in is on, choose a chromosome from the list, then click on "Search". It is not recommended to choose the default ("Any chromosome"), as the resulting search will result in a large number of loci. If you don't know which chromosome your locus of interest is on, you may want to perform a search by locus rather than a search for frequencies.
  After you choose a chromosome, a list of loci typed on that chromosome appears. Click in the box to the left of the locus (loci) name(s) you are interested in, then click on "Show populations for these loci". A list of populations will appear.

  All of these populations have been typed for one or more of the loci you have chosen. Choose the population(s) you are interested in the same way you previously chose loci by checking their appropriate boxes. Click on "Show frequencies for these populations and loci".
  A page will come up to a) verify you are satisfied with the loci and populations you chose, and b) determine what information you want reported (which fields and how many records at a time).

  Finally, click on "Search for frequencies", and a table of frequencies will appear as if you had entered these search specifications into the main frequency search page.

• Search for frequency records by population

  Searching for frequency records by populations works the same way as searching by loci, only you can chose populations first and then chose loci which have been typed for one or more of those populations. To search by population, click on the "Show all" after the "Population" field on the main frequency search page.

After a frequency table comes up, you'll note some of the text is in a different color. For example, the locus name may appear in blue or purple while the rest of the text is in black. The colored text is a link to a page of more detailed information. Specific examples follow.

• Locus

  Clicking on the locus name from a frequency search provides a page of information on the locus, such as ADH1B. The information may include the locus name and symbol, chromosome, chromosomal band position, and citation information. Where possible, citations will point to a relevant PubMed record which may include a link to the publisher's full text article. A list of polymorphic sites typed on this locus will also appear. By clicking on the site name, detailed information about the site will appear. You may also chose to search for all frequency records related to this locus in either table or semicolon delimited format.

• Polymorphism

  By clicking on the polymorphism name, detailed information appears about the site, such as the ADH1B Intron 3 RsaI site. Information presented may include the Polymorphism name, the Locus name and a link to the detailed locus information, the Locus symbol, a brief description of the site, the typing method used to type the site, a table of alleles in the database for that site, the ancestral allele, how the ancestral allele was determined, citation information, the typing protocol used, and a histogram of allele frequencies in various populations. Where histograms are present, they are also represented independently on the Kidd Lab Histogram page. Where typing protocols are available, they will be present on the Kidd Lab Protocol page when it becomes available. As with the detailed locus information, you can choose to search for all frequency records related to this polymorphic site in either tabular or semicolon delimited formats.

• Population

  Clicking on the population name brings up a page of detailed information about that population and the samples from that population in the database, such as for the Danes. Information about the population includes the population name, a short description where available, and representative longitude and latitude where available. Sample information can include an internal "Sample ID", a sample descriptions, the number of individuals in the sample, and citation information. Again, you can chose to search for all frequency records for this population in tabular or semicolon delimited formats.

You may wish to search for frequency information for a locus and not know the locus name or chromosome. Maybe you just want detailed information about a locus without doing a full frequency search. In either case, you can chose to search for a locus by chromosome. From the main index page, choose "Search for a locus". Then you just have to move your mouse over the chromosome name on the left to bring up a list of loci from that chromosome in the database on the right. If you then move your mouse to the right frame and click on a locus name, detailed information about that locus will appear. Similar pages are in preparation for populations.

© 2012 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

Last updated 1/21/02.