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Table 1 Binary patterns for nucleotides, A, U, C, G, and a loop/bulge structure, denoted by L, in PHDCleav [14] and LBSizeCleav with k ones based on sequences and predicted secondary structures

From: LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length

Mapping   Sequence Structure
PHDCleav A [1,0,0,0] [1,0,0,0]
  U [0,1,0,0] [0,1,0,0]
  C [0,0,1,0] [0,0,1,0]
  G [0,0,0,1] [0,0,0,1]
  L [0,0,0,0]
Extended PHDCleav A [1,0,0,0,0]
  U   [0,1,0,0,0]
  C   [0,0,1,0,0]
  G   [0,0,0,1,0]
  L   [0,0,0,0,1]
LBSizeCleav A [1,0,0,0,0, … 0]
  U   [0,1,0,0,0, … 0]
  C   [0,0,1,0,0, … 0]
  G   [0,0,0,1,0, … 0]
  L   \([0, 0, 0, 0, 0, \dots, 0, \overbrace {1, \dots, 1}^{k}, 0, \dots ]\)
  1. In PHDCleav binary patterns each nucleotide is represented by a 4-dimensional vector, and in PHDCleav Extended patterns each nucleotide is represented by a 5-dimensional vector, while in LBSizeCleav the dimension of the vector is 3+k+N, in which N denotes the maximum number of length of loop/bulges among all the pre-miRNAs in the training dataset
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