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KEY-STRING MINIMUM-DIVERGENCE DIAGRAM |
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Author: Matko Gluncic (matko@phy.hr)
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If you use KEY-STRING MINIMUM-DIVERGENCE DIAGRAM 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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With Key-string Algorithm Divergence Method we construct N divergence diagrams for each referent monomer. Now we assign to each of N referent subsequences a minimal value of its divergence with respect to all other subsequences. We display graphically these minimal values of divergence along the divergence array, depending on the enumerator k of referent subsequences. For example, if the minimal value of all divergences in the divergence diagram for the kth referent subsequence is d, then the corresponding point in the KSA minimum-divergence diagram is a point with horizontal coordinate k and vertical coordinate d. Finally, in order to reduce some local fluctuations in the above diagram, we perform an additional averaging in this diagram as follows. Let us consider a minimal divergence d that corresponds to the kth referent subsequence. We form a neighboring interval of referent subsequences, for 10 neighboring integers smaller than k (ie, for k-10, k-9, ... k-1) and for 10 neighboring integers larger than k (ie, for k+1, k+2, ... k+10). If there is at least one divergence less than 3% in the intervals on both sides of k, then we assign 0 instead of d to the kth referent subsequence. Otherwise, the computed value d is left unchanged. A diagram obtained in this way is referred to as the KSA minimum-divergence diagram. Thus, in the KSA minimum-divergence diagram the domain of HORs is directly identified as the interval with a straight line along the horizontal axis. |
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