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Consensus higher order repeats and frequency of string distributions in human genome

Our Key String Algorithm is used as robust method for effective identification and structural analysis of genomic sequence in NCBI sequence of human genome. We have developed a method, using total frequency distribution of all r-bp key strings in dependence on fragment length l to determine the exact size of all repeats within a given genomic sequence, both monomeric and HOR-type. In this way we determine the dominant key string, optimal for segmentation of a given genomic sequence into repeat units. We show that a wide class of 3-bp key strings generates a key-string-dependent periodic cell which provides a simple identification and consensus length determination of HORs, or any other highly convergent repeat , both tandem or dispersed. We illustrate KSA application for HORs in human genome and determined consensus HORs in the Build assembly. We compute the suprachromosomal family classification and CENP-B box/ pJalpha distributions for HORs. We introduced a flexible 28-bp key string which reveals both monomeric alpha satellites and alpha monomer segmentation of internal HOR structure. We identified in the Build 36 assembly a highly convergent 3434-bp long monomer in chromosome 5 (divergence less than 0.3%).

DNA; human genome; higher order repeat; key string algorithm; consensus; frequency of string distribution

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