UNBIASED, K-MER BASED ANALYSIS OF DIFFERENTIALLY PRESENT REPETITIVE ELEMENTS BETWEEN MOUSE SPECIES
In: Student Reports, Summer 2019, The Jackson Laboratory
Dr. Beth Dumont
Repetitive DNA elements have previously been considered "junk DNA" because they are not protein coding, but there is increasing evidence that many have impacts on the organisms that they inhabit. In this project, we manipulated tables of DNA k-mer frequencies for 59 diverse mouse genomes to reveal which k-mers varied most in frequency between genomes. This analysis revealed sets of differentially present, highly abundant k-mers that could be assembled into longer sequences. One sequence, seq A. had a number of notable attributes, such as an inverse repeat structure and consistent pattern of presence inside of known transposable elements. We began exploring these sequences to reveal routes for future study conducted a PCR consistent with the differential presence of seq A between mouse strains in vitro.
Charlebois, Caleigh, "UNBIASED, K-MER BASED ANALYSIS OF DIFFERENTIALLY PRESENT REPETITIVE ELEMENTS BETWEEN MOUSE SPECIES" (2019). Summer and Academic Year Student Reports. 2645.