Author: Gao, James ZM; Li, Linda YM; Reidys, Christian M
Title: Inverse folding of RNA pseudoknot structures Document date: 2010_6_23
ID: 1lojd0xa_18
Snippet: Note, however, that a p-neighbor has either Hamming distance one (G-C ↦ G-U) or Hamming distance two (G-C ↦ C-G). We call a u-or a p-neighbor, y, a compatible neighbor. In light of the adjacency notion for the set of compatible sequences we call the set of all sequences folding into S the neutral network of S. By construction, the neutral network of S is contained in C [S]. If y is contained in the neutral network we refer to y as a neutral n.....
Document: Note, however, that a p-neighbor has either Hamming distance one (G-C ↦ G-U) or Hamming distance two (G-C ↦ C-G). We call a u-or a p-neighbor, y, a compatible neighbor. In light of the adjacency notion for the set of compatible sequences we call the set of all sequences folding into S the neutral network of S. By construction, the neutral network of S is contained in C [S]. If y is contained in the neutral network we refer to y as a neutral neighbor. This gives rise to consider the compatible and neutral distance of the two sequences, denoted by C(s, s′) and N(s, s′). These are the minimum length of a C[S]-path and path in the neutral network between s and s′, respectively. Note that since each neutral path is in particular a compatible path, the compatible distance is always smaller or equal than the neutral distance.
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