TMO: time and memory optimized algorithm applicable for more accurate alignment of trinucleotide repeat disorders associated genes

ABSTRACTIn this study, time and memory optimized (TMO) algorithm is presented. Compared with Smith–Waterman's algorithm, TMO is applicable for a more accurate detection of continuous insertion/deletions (indels) in genes’ fragments, associated with disorders caused by over-repetition of a certain codon. The improvement comes from the tendency to pinpoint indels in the least preserved nucleotide pairs. All nucleotide pairs that occur less frequently are classified as less preserved and they are considered as mutated codons whose mid-nucleotides were deleted. Other benefit of the proposed algorithm is its general tendency to maximize the number of matching nucleotides included per alignment, regardless of any specific alignment metrics. Since the structure of the solution, when applying Smith–Waterman, depends on the adjustment of the alignment parameters and, therefore, an incomplete (shortened) solution may be derived, our algorithm does not reject any of the consistent matching nucleotides that can be in...