Identifying nonrandom occurrences of simple sequence repeats in genomic DNA sequences.
Numerous disorders, including prostate cancer and muscular dystrophy, have been associated with nonrandom occurrences of certain simple sequence repeats (SSRs) found in genomic DNA. In a previous paper, we introduced probabilistic methods for identifying such SSRs that possess nonrandom distribution profiles. Here, we apply these methods to the distribution profiles of SSRs of monomers, dimers, trimers, and tetramers occurring in the human genomic sequence data. In particular, we show that the nonrandomness of SSRs is an exponential function of SSR length. We also demonstrate the existence of threshold SSR lengths for the significant nonrandomness (specifically, under/over-representation) of SSRs. These results are consistent with previous findings and demonstrate the potential use of the previously derived probabilistic methods in the identification of (putative disease associated) SSRs that exhibit significant deviations from random expectations.
Ndifon
Wilfred
W
Department of Biology, Morgan State University, Baltimore, Maryland 21251, USA.
Nkwanta
Asamoah
A
Hill
Dwayne
D
D001483:Base Sequence / Q000235:genetics*; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics*; D015233:Models, Statistical; D014481:United States