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


What this document contains:

Navigating the database

Navigating this database is as simple as navigating any web page. Some text will be a different color from other text. Generally, these are links to more information. For instance, after generating a search, you will see the name of the locus the polymorphic site is located at. The text of the locus name should be in a different color from the text of the header. If you click on a locus name, a new page will come up with information about the locus, including relevant citations if available. To go back to the previous page, you can always click on the "Back" button on your browser. If your browser has sufficient cache space enabled (generally true with default settings), any selections you made to the previous page should be restored.

Making a query

Making a basic query takes just a few simple steps. First, decide which fields you wish information on and fill in the search term in the text box. For instance, if you want information on all the sites in the Tryptophan Hydroxylase (TPH) region in the database, enter "TPH" in the "locus symbol" text box. In general a more productive search will result from using the "symbol" fields (locus symbol, allele symbol) than the corresponding fields for the full name. Wildcard searches will be even more productive (see "Searching for Multiple Terms" below). Searching is case-insensitive (the search doesn't distinguish between upper and lower case).

When more than one field is used, the search combines the material with a logical "and". For example, "D%" in the "Locus Name" field, 17 in the Chromosome pulldown menu, and "%pygmy" in the population field will retrieve all the D segments in the Biaka and Mbuti pygmies that are located on chromosome 17.

Next, decide what information you want to see in the resulting table by putting a check in the box to the right of the field name in the area marked "Display" (located at the bottom of the search page). The fields "Population Name", "Locus Name", "Polymorphism Name", "Frequency", and "Sample Size" are always checked by default.

Decide if you want "semicolon delimited text" or a simple table. To generate semicolon delimited text, check the box to the right of the text "Semicolon Delimited Text?". If you wish to import the resulting data into a spreadsheet, use the delimited text. If your spreadsheet does not recognize a semicolon as a delimter, copy the information into a word processor and change all semicolons to the desired delimiter. If you just want to view the results or print them and don't need to import the data elsewhere, don't chose the delimited text as that format will be confusing to read.

Finally, click on the button labelled "Search", and your query results will come up.

List all populations and loci

When using the database, you may not know the exact name of the population or locus you are looking for. To list all loci or populations, click on the link "list all" to the right of their respective fields in the main query page. A list of loci or populations will appear. You can click in the checkbox for the particular locus (loci) or population(s) you are interested in. Next, you can chose which populations (for loci) or loci (for populations) typed for the previously chosen loci or populations you wish to see frequency data for. This search uses a logical "or" within populations and loci, and a logical "and" between groups of loci and populations.

Searching for multiple terms within a field

Searching for multiple terms can be accomplished by either or both of two methods.

First, you can list two or more terms separated by a comma. As an example, if you want to find the ADH2 and TPH loci, you can enter "ADH2, TPH" in the locus symbol field. Fields where this can be used include locus name, locus symbol, band position, polymorphism name, allele name, allele symbol, polymorphism description, and population.

Secondly, you can use a "wildcard" character ("%") to find any terms containing the text. The wild card character can be thought of as saying "insert anything here". To fnd all loci whose symbol starts with ADH, enter "ADH%" in the "locus symbol" area. To find all loci whose symbol ends in "3", enter "%3" in the "locus symbol" area. To search for any locus whose name includes "dehydrogenase" in the locus name, enter "%dehydrogenase%" in the "locus name" area.

Searching for ranges of frequencies

A search for a range of frequencies can be accomplished using the standard mathematical symbols >, <, and =, as well as a hyphen. To find any entries with a frequency greater than a certain value (e.g. 0.45), use the greater than sign (">") or the greater than or equal to sign (">=") which finds all frequencies greater than or equal to a frequency (e.g. ">=0.45" finds all frequencies greater than or equal to 0.45). Correspondingly, values less than a certain value can be found using the less than sign ("<") or the less than or equal to ("<="). To find frequencies within a certain range (e.g. between 0.45 and 0.55), use the hyphen (e.g. "0.45-0.55").

Band Position

This is NOT currently a "calculated" value, but only a text field. Therefore, use of this field will only give exact matches or "wildcard" matches. Thus, "17q%" will find anything on 17q, but will not find a locus assigned to the interval 17p11-q11.

Finding more help

© 2008 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 since 2002 and maintenance by Haseena Rajeevan

Last updated 1/21/02.