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University of Louisville Bioinformatics

Bioinformatics Research at the University of Louisville


Project:

Web-Based Publication of Genetic Information for DNA-Based Animal Forensics in U.S. Livestock


Authors:

Ted Kalbfleisch(1), Joe Morris (2)
Nevine Eltonsy(1),  Eric Rouchka(2)

  1. University of Louisville Center for Genetics in Molecular Medicine (CGeMM)
  2. University of Louisville Center Department of Computer Engineering and Computer Science
Motivation:
Single nucleotide polymorphisms (SNPs) can be used to generate DNA-based fingerprints for individual identification. The efficiency of DNA fingerprinting is greatest when the frequency of both SNP alleles is near 0.50. A number of SNPs have been identified in cattle populations with minor allele frequencies (MAF) greater than 0.40. Genotypes from those SNPs can be used to track tissues, trace animal origin, and determine parentage. In order to make this data accessible to scientists who are interested in developing assays for inexpensive genotyping tests, it has become necessary to develop a web services based system that will store, retrieve, and analyze the data being experimentally generated. This data includes breed information for the cattle analyzed, upstream and downstream flanking sequence for the SNPs, and trace data for confirmation of the genotype calls which led to the SNP discovery. This data will be available through web services application programming interfaces (APIs) such that it is straightforward to write independent third party applications that utilize the data. It is hoped that this system will prove an invaluable tool for SNP and genotype based research and, in the future, will be extended beyond its present intentions.
Results:

Web Site: http://cgemm.louisville.edu/usmarc/MARC_web_page/traceback.html

Research currently underway.

Supported by a subcontract from Clinical Data, Inc. under USDA SCA No. 58-5843-385


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