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ALFRED


NAR Molecular Biology Database Collection entry number 119
Rajeevan, Haseena1,2; Soundararajan, Usha1; Kidd, Judith1; Pakstis, Andrew1; Kidd, Kenneth1
1Department of Genetics, Yale University School of Medicine, 333 Cedar Street, PO Box 208005, New Haven, CT 06520-8005, USA
2Center for Medical Informatics, Yale University School of Medicine, 333 Cedar Street, PO Box 208009, New Haven, CT 06520-8009, USA

Database Description

ALFRED (the Alelle FREquency Database) is designed to store and disseminate frequencies of alleles at human polymorphic sites for multiple populations, primarily for population genetics and molecular anthropology communities. The emphasis remains on populations typed for multiple polymorphisms and polymorphisms typed on multiple populations. Allele frequencies at each site are linked to the specific populations and specific samples of those populations with descriptions. When available haplotype frequencies are also included. Several new features have been added to ALFRED in the past year, besides the increased quantity and quality of data in the database. ALFRED now has information on 796 polymorphic sites typed on at least one population sample and 357 populations typed for at least one polymorphism. Effort was also put into enhancing the data accessibility feature of ALFRED. ALFRED is accessible from http://alfred.med.yale.edu/.

Recent Developments

I>Data accessibility and submission
Data for individual polymorphisms can be displayed in graphic, table, and semi-colon delimited (for downloading) formats. In addition, the entire database can now be downloaded in XML format by following the link provided in the web site (http://alfred.med.yale.edu/alfred/xmldatadump.asp). The DTD (Data Type Definition) developed is also provided for download and use for the validation of the XML files. Twice a month the XML files are updated. Depending on requirements, a researcher can download the entire database with or without the descriptions or have the tables separately downloaded in XML format.

A web page has been prepared for the purpose of providing guidelines to users for submitting data to ALFRED (http://alfred.med.yale.edu/alfred/AboutALFRED.asp#datasubmission). The excel spreadsheet provided for download can be used for submitting data to ALFRED.

Additional Information Button
A new icon has been introduced for displaying additional information pertaining to any particular output. Currently, it is accessible with the frequency values. Clicking on the icon will take you to a page displaying the typing method used and the citation of the publications the frequency data were retrieved from.

Search for frequency by author's name
We have introduced a new function in ALFRED. The Basic Search link (http://alfred.med.yale.edu/alfred/basicsearch.asp) will take you to the Basic Search page, which has a section 'Search for Publication using author's last name'. If you want to retrieve the frequency data from a particular publication or even want to find out if frequencies from a particular publication are in ALFRED, type in the last name of any of the authors in the provided space. You will see a list of the publications that include the author you are searching for. By clicking the button to the left of the publication you will retrieve a list of sites with frequency data that have been entered into ALFRED from that publication.

Graphical overview of the database
The graphical overview page has two new links, one of which is 'sites per population ordered by number of sites', which shows the number of allele frequency tables for each population listed in descending order (http://alfred.med.yale.edu/alfred/popspersite_graphbycount.asp). Currently the maximum is 562 for the Japanese. The other is 'populations per site ordered by number of populations' (http://alfred.med.yale.edu/alfred/sitesperpop_graphbycount.asp) which represents the number of allele frequency tables for each polymorphic site listed in descending order. Currently the maximum is 129 for PLAT TPA25 Alu insertion.

Registration and newsletter
ALFRED now has a page dedicated for user registration (http://alfred.med.yale.edu/alfred/registration.asp). The primary objective for collecting personal information from the users is to be able to mail to users the ALFRED Newsletter with highlights and recent additions to ALFRED on a regular basis.

Acknowledgements

Ongoing funding of ALFRED is provided by NSF grant BCS0096588. Initial funding for ALFRED was provided by NSF grant SBR-9632509 and USPHS grants P01GM57672, R01AA09379, and T15LM07056.


Go to the abstract in the NAR 2012 Database Issue.
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