Efficient GPU-accelerated extraction of imperfect inverted repeats from DNA sequences

Inverted Repeats in DNA sequences have long been known to have both major beneficial and detrimental effects in regards to how DNA is transcribed and duplicated. Palindromic sequences are frequently translated into proteins and may also facilitate DNA repair in some instances. However, they are also associated with significantly increased risk of mutation. Current methods are either slow or limited in the ways they can process imperfections due to tradeoffs between computational complexity and completeness in results. Our method allows for the efficient extraction of imperfect inverted repeats, featuring the ability to define the level of imperfection by the proportion of mismatching bases. By using GPU acceleration, we achieve order of magnitude speedups compared to the current leading method for imperfect inverted repeat extraction while allowing for more flexible results. We conducted a study on protein-coding exons contained entirely within inverted repeats. We found that these exons were significantly more likely to be included in multiple gene transcripts and were less likely to be spliced out.