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SEGMENTATION KEY-STRING |
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Author: Matko Gluncic (matko@phy.hr)
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If you use SEGMENTATION KEY STRING as a tool in your published research, we ask that the
following reference be cited: Rosandic, M., Paar, V., Gluncic, M., Basar, I., Pavin, N. |
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The principle of the computational KSA is analogical to the principle of restriction enzyme method: the computational KSA procedure can "cut" genomic sequence into alpha monomers or into HORs, depending on the proper choice of the key string, which could be considered analogous to a computationally simulated "enzyme". The KSA method is organized in 5 steps, as follows: 1. Selection of a short string of nucleotides (three to six), referred to as the key string. 2. Computational segmentation of a given genomic sequence into subsequences, referred to as key-string subsequences, each starting with the key string. 3. Formation of an array of lengths of key-string subsequences (length-array) in the order of appearance. 4. If present, periodic HORs can easily be identified by naked-eye inspection of the length-array formed in the third step. 5. Deviations from periodic repetitions in the length-array are used for an easy and robust direct identification of insertions, deletions and point mutations with respect to an ideal HOR structure. |
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