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ALFRED : the AL lele FRE quency D atabase

ALFRED : the AL lele FRE quency D atabase. H. Rajeevan 1 , M.V. Osier 1 , K. Cheung 2 , H. Deng 1 , L. Druskin 2 , J.R. Kidd 1 , S. Stein 1 , A.J. Pakstis 1 , N.P. Tosches 2 , P.L. Miller 2 , K.K. Kidd 1.

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ALFRED : the AL lele FRE quency D atabase

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  1. ALFRED:theALleleFREquencyDatabase H. Rajeevan1, M.V. Osier1, K. Cheung2, H. Deng1, L. Druskin2, J.R. Kidd1, S. Stein1, A.J. Pakstis1, N.P. Tosches2, P.L. Miller2, K.K. Kidd1 1Dept. of Genetics and 2Center for Medical Informatics, Dept. of Anesthesiology, Yale University School of Medicine, New Haven, CT, 06520-8005, USA.

  2. ALFRED Home Pagehttp://alfred.med.yale.edu/

  3. Overview ALFRED,theALleleFREquencyDatabase, is designed to serve as a central repository of allele frequencies for DNA sequence variation in the human genome–curated and cross referenced to molecular and ethnographic databases–by assembling in one place data that are dispersed very widely in the scientific literature. The emphasis is on data from anthropologically defined populations. Who’s Looking at ALFRED? ALFRED receives hits from approximately 600 unique hosts per month. These originate from many different countries.

  4. ALFRED is designed to provide: • allele frequencies and information on a wide range of loci, polymorphic sites, populations, and samples. • reference of frequencies to a specific typing protocol for a specific polymorphism at a specific locus. • reference of frequencies to a specific sample of a specific population with descriptions and links to additional documentation/description. • different search/retrieval options/pathways for frequencies. • increased flexibility in display of frequencies. • XML data dump (with DTD) of the entire database.

  5. Polymorphism Information

  6. Population Information

  7. Frequency search result – tabular format The icon is used throughout ALFRED whenever additional information can be provided. Click here to get additional information

  8. Frequency search result – graphical view Clicking here will give you population information Clicking here will give you sample information Haplotype frequencies displayed as a stacked-bar histogram with the legend for colors at the bottom of the page

  9. Graphical Overview of ALFRED A. Populations per site • Ordered by number of population’s typed (Multiple different samples of a population are not distinguished in this summary)

  10. B. Sites per population • Ordered by number of sites typed (Multiple different samples of a population are not distinguished in this summary)

  11. XML data dump of the database

  12. The ALFRED Team Senior Faculty Kenneth K. Kidd, Ph.D., Professor of Genetics and Psychiatry (ALFRED P.I.) Perry Miller, M.D., Ph.D., Director of Center for Medical Informatics Curators Hongyi Deng, M.S., Research Associate Shannon Stein, B.S., Research Assistant Programmers Haseena Rajeevan, Ph. D., Systems Programmer Nicholas P. Tosches, M.D., Associate Research Scientist Lyudmila Druskin, M.D., Postdoctoral Fellow and Associate Consultants Andrew J. Pakstis, Ph. D., Research Scientist Judith R. Kidd, Ph. D., Research Scientist Kei-Hoi Cheung, Ph. D., Assistant Professor ALFRED is supported by the U.S. National Science Foundation

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