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

ALFRED FAQ

General
Polymorphism
Population
Searching ALFRED
Data downloads from ALFRED
Data submission to ALFRED
Use of ALFRED
Citing ALFRED
Submit a question


General

What is ALFRED?

ALFRED (The ALlele FREquency Database) has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases. More

How often is ALFRED updated??

ALFRED is updated on a daily basis.

Where can I find the source of the frequency data that is in ALFRED?

The icon in the frequency display will lead you to the citation of the publication the frequencies were extracted from.

Where can I find the typing method for a particular allele frequency data that is in ALFRED?

Clicking on the icon next to the particular allele frequency data in the frequency display will give you the typing method information. For detailed typing protocol information, you can find this from the publication listed in the same Additional Information page of ALFRED.

Are ALFRED UIDs linked to dbSNP rs#s and ss#s ?

dbSNP rs# and ss#s are not explicitly displayed in the ALFRED SNP Information page. But we provide links to dbSNP pages from each ALFRED Polymorphism Information page. You can aslo search ALFRED using dbSNP rs and ss#s using the keyword search function.
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Polymorphism

How do you name polymorphisms in ALFRED?

Since allele frequency data are extracted from published literature by ALFRED curators, in general the polymorphism name in ALFRED is the same as the name from the literature. If a polymorphism is addressed differently by different authors, we pick the most common one as the primary polymorphism name in ALFRED and the remaining names for this polymorphism are entered as Synonyms.

What are the different types of Polymorphisms addressed in ALFRED?

There are STRPs (short tandem repeat polymorphisms), VNTRs (variable number tandem repeat polymorphisms), SNPs (single nucleotide polymorphisms), INDELs (insertion/deletion polymorphisms), and RFLPs (restriction fragment length polymorphisms) in ALFRED. ALFRED also contains haplotype data.

Why are there different versions for the same polymorphism?

If different nomenclatures are used by different authors for the alleles of the same polymorphism, integration of the alleles becomes difficult. In that case the polymorphisms are entered as separate versions of the same polymorphism. For example there are 3 versions of 3' VNTR of APOB.

Which databases are loci and polymorphisms cross-referenced to?

Usually loci are cross-referenced to LocusLink, OMIM, GDB, GenBank, PubMed, CHLC, CEPH, UniSTS, LSDBs (locus specific databases) along with other related resources. Polymorphisms are cross-referenced to GDB, GenBank, dbSNP, CHLC, CEPH along with other related resources.

Is there any redundancy in polymorphism entries in ALFRED?

The curators make every effort to enter each polymorphism into ALFRED only once, though allele frequencies for a polymorphism may be extracted from many publications. However, since the nomenclature used for polymorphisms and alleles is not consistent in the literature we may have some redundancy with regards to polymorphisms.

Why are some of the descriptions missing? How can I find this information?

Detailed descriptions may be missing for some of the populations, loci, and polymorphisms. Because ALFRED staff want to maintain a high quality of information in ALFRED these descriptions require extensive research. Unfortunately new populations, loci, and polymorphisms are being added to ALFRED faster then ALFRED staff can adequately research and describe them. If there is a population, locus, or polymorphism you are interested in that does not have a description and you would like more information contact ALFRED staff at alfredcurate@krunch.med.yale.edu and we will do our best to accommodate your request.

In frequency search results why do I see sample duplication. Like two samples for the same population but with same sample size and same frequencies for the same allele?

This may be a case where the frequencies for the two samples were extracted from two different publications. ALFRED curatorial staff do their best to extract allele frequencies from the published literature. If the papers are from the same lab, this might be a case of sample duplication. Before data is uploaded into ALFRED, the corresponding authors are contacted in case of conflicting or erroneous data. If you are using data from ALFRED for analysis purposes and come across data duplications or other ambiguities we advise you to consult the original author for clarification. Every frequency in ALFRED is linked to the publication it was extracted from.
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Population

What is the difference between a population and a sample?

A population is the total number of individuals belonging to a defined group and the sample is a selected segment of that population.

How are the geographic regions divided?

The geographic regions are divided strictly on an arbitrary basis. The divisions are used only to facilitate browsing of the large number of populations ALFRED currently has.

Why are some of the descriptions missing? How can I find this information?

Detailed descriptions may be missing for some of the populations, loci, and polymorphisms. Because ALFRED staff want to maintain a high quality of information in ALFRED these descriptions require extensive research. Unfortunately new populations, loci, and polymorphisms are being added to ALFRED faster then ALFRED staff can adequately research and describe them. If there is a population, locus, or polymorphism you are interested in that does not have a description and you would like more information contact ALFRED staff at alfredcurate@krunch.med.yale.edu and we will do our best to accommodate your request.

In frequency search results why do I see sample duplication. Like two samples for the same population but with same sample size and same frequencies for the same allele?

This may be a case where the frequencies for the two samples were extracted from two different publications. ALFRED curatorial staff do their best to extract allele frequencies from the published literature. If the papers are from the same lab, this might be a case of sample duplication. Before data is uploaded into ALFRED, the corresponding authors are contacted in case of conflicting or erroneous data. If you are using data from ALFRED for analysis purposes and come across data duplications or other ambiguities we advise you to consult the original author for clarification. Every frequency in ALFRED is linked to the publication it was extracted from.
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Search

How can I search ALFRED for a particular SNP?

There are 3 different ways a user can search ALFRED for a particular SNP. The options are Basic Search, Loci and Keyword Search. If you know the ALFRED UID of the SNP, enter that in the Basic search page and click 'Search for UID'. If you know the chromosome and gene the SNP resides in, enter Loci option in the Search Category and follow the links to the particular SNP. If you are not sure about the exact chromosome and do not know the UID, use the Keyword Search option and type in the SNP name and search the database.More

Can I have an example search for frequencies and other entries?

Example Search
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Data downloads from ALFRED

What are the different formats I can download allele frequency data from ALFRED?

From the section 'downloads' under the 'Summaries Tab'all the primary tables in ALFRED can be downloaded in XML format. Semi-colon delimited frequency files for individual sites or individual populations can be downloaded from respective information pages just by selecting the check-box available at the begining of the page and clicking the 'Retrieve Frequencies' button.

How can I convert the XML files to tab delimited or semi-colon delimited format files?

There is no easy way to convert XML files to tab delimited files or semi-colon delimited files. With an XML eXtensible Stylesheet Language (XSL) template or transformation file, you can convert an XML document into a different (usually HTML-compliant) format. ALFRED programmers are working on providing the data in different formats.

How can I convert the semi-colon delimited format files to tab delimited format files?

Copy and paste the displayed semi-colon delimited format files in a notepad and save it as a text (file.txt) file. Then open the text file in an Microsoft Excel Program and save it as tab delimited file.
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Data submission to ALFRED

What are the criteria for entering data into ALFRED?

Criteria for Data Entry into ALFRED

How can I submit data to ALFRED?

The section Data submission to ALFRED in About ALFRED will help you with information needed to submit frequency data to ALFRED. You can also contact our staff to assist you.
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Use of ALFRED

Can I include ALFRED into a Lab course I am writing for an undergraduate genetics laboratory?

ALFRED is intended to be a useful scientific resources to everybody, so we welcome you having your students use the database. In fact, if you think there is something we can do to make it a more useful didactic tool, please send us your suggestions.

In frequency search results why do I see sample duplication. Like two samples for the same population but with same sample size and same frequencies for the same allele?

This may be a case where the frequencies for the two samples were extracted from two different publications. ALFRED curatorial staff do their best to extract allele frequencies from the published literature. If the papers are from the same lab, this might be a case of sample duplication. Before data is uploaded into ALFRED, the corresponding authors are contacted in case of conflicting or erroneous data. If you are using data from ALFRED for analysis purposes and come across data duplications or other ambiguities we advise you to consult the original author for clarification. Every frequency in ALFRED is linked to the publication it was extracted from.

Why do I see different data represented in the graphical format and tabular format?

The ALFRED database and the user interface is designed in such a way that when allele frequencies are first uploaded into the database, only the graphical format display code of the user interface will be accessing the new tables. The table accessed by the tabular format display code is updated only once a day. This is done around 6AM (US Eastern Time). Therefore, there is always a time lag of few hours between a new allele frequency upload and update of the tabular format tables. This arrangement is essential for the optimal performance of ALFRED Public Interface.
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Citing ALFRED

How should I cite ALFRED?

Use http://alfred.med.yale.edu for URL citing and papers

a. Osier MV, Cheung KH, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. "ALFRED: an allele frequency database for diverse populations and DNA polymorphisms--an update." Nucleic Acids Res. 29(1):317-9. (2001)

and/or

b. Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL, Kidd KK. "ALFRED the ALlele FREquency Database update." Nucleic Acids Research..31(1):270-271.(2003) pdf file of article

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Submit a question

If you would like to see a question addressed in this section, please type-in the question and click 'SUBMIT'.
YOUR QUESTION:
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© 2018 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 Modified 3/7/2011 11:10:18 AM