This is the program for the 2010 Joint Statistical Meetings in Vancouver, British Columbia.

Abstract Details

Activity Number: 681
Type: Contributed
Date/Time: Thursday, August 5, 2010 : 10:30 AM to 12:20 PM
Sponsor: Section on Statistical Computing
Abstract - #306668
Title: Moments of Strings of DNA Bases
Author(s): Robert J. Blodgett*+ and Errol Strain
Companies: FDA and FDA
Address: 5100 Paint Branch Parkway, College Park, MD, 20740,
Keywords: repeats ; genomic ; recursive equations
Abstract:

Repeats in genomic DNA usually are identified either using a dictionary of known repeats or through pairwise comparisons of the sequence to itself. We propose an alternative method for finding repeats based on the moments of the distribution for nucleotide frequencies in substrings of the genome. Given equal frequencies of the A, C, G, and T nucleotide bases, the number of times a short string of these bases occurs will have a distribution. The moments of this distribution can be found by solving a systen of recursive equations. Our application focuses on identifying repeats in bacterial genomes. These repeats often make good targets for typing assays, and they may also play a role in differences in pathogenicity among different bacterial strains.


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