Title

UNBIASED, K-MER BASED ANALYSIS OF DIFFERENTIALLY PRESENT REPETITIVE ELEMENTS BETWEEN MOUSE SPECIES

Document Type

Article

Publication Date

Summer 2019

JAX Location

In: Student Reports, Summer 2019, The Jackson Laboratory

Abstract

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.

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