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Bioinformatics Advance Access published online on January 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg446
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 19, 2003
Accepted September 17, 2003

Applications note

Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers

Tu H. Nguyen 1*, Chunyu Liu 2, Elliot S. Gershon 1, Francis J. McMahon 3

1 Department of Psychiatry, University of Chicago, USA
2 Department of Psychiatry, University of Chicago; National Laboratory of Medical Genetics of China, Central South University, Changsha Hunan, 410078, P.R. China
3 Mood and Anxiety Disorder Program, National Institute of Mental Health, National Institutes of Health, Dept. of Health and Human Services, Bethesda, MD, USA

* To whom correspondence should be addressed. E-mail: tnguyen{at}yoda.bsd.uchicago.edu.


  Abstract

Publicly-available single nucleotide polymorphism (SNP) allele frequencies are an important resource for the selection of genetic markers that may be most useful for gene mapping and association studies. Data mining these allele frequencies through disparate public databases and web sites is time consuming and can result in inconsistent findings. We have developed a web-based software tool, Frequency Finder, to acquire SNP allele frequencies from multiple public data sources and return a summarized result to the user. Our software optimizes and automates the search of candidate markers, decreasing the amount of time it would take to extract pertinent data manually. We have included several methods to output the data, including on-screen and as a compressed text file. We show that Frequency Finder accurately retrieves available frequency data from the available sources. Using this tool, we detect significant differences between Asian, African, and Caucasian populations in the allele frequency spectra of 246,097 SNPs. While limited to public databases that provide web-based access to allele frequencies, Frequency Finder provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources. Frequency Finder is available for public use at http://mapgenetics.nimh.nih.gov/frequencyfinder and at http://bluegenes.bsd.uchicago.edu/frequencyfinder.


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SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)
Bioinformatics, May 15, 2005; 21(10): 2517 - 2519.
[Abstract] [Full Text] [PDF]


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