engleski

Key-string Algorithm - Novel approach to computational analysis of repetitive sequences in human centromeric DNA

We introduced a novel computational approach, Key-string Algorithm (KSA), for the identification and analysis of arbitrarily large repetitive sequences and higher order repeats (HORs) in non-coding DNA. Our approach is based on the use of key string that plays a role of an arbitrarily constructed "computer enzyme". In this framework we introduced and developed, on the basis of a combination of computations on a very modest scale, by eye inspection and graphical display of results of analysis. Sequence analysis software was developed, containing seven programs for KSA-related analyses (KSA segmentation, colorHOR diagram, KSA-divergence method, 171-bp subsequence-convergence diagram, KSA minimum-divergence diagram, total frequency distribution of KSA subsequence lengths, four-symbol fast Fourier transform). This approach was demonstrated in the case of alpha satellites and HORs in the human genetic sequence AC017075.8 (193277 bp) from the centromeric region of human chromosome 7.

centromere; chromosomes; human pair 7; computational biology; DNA satellite; Fourier analysis; molecular sequence data; repetitive sequences; nucleic acids; point mutation

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