EDscan (Energy difference scan): A program for discovering well-ordered folding segments in nucleotide sequences. The computer program EDscan is designed to calculate z-score Zscre of local segments in a sequence. The standardized z-score Zscre is defined as:
Zscre = (Ediff - Ediff(w))/stdw,
where Ediff of a local segment is Ediff = Ef - E, E is the lowest free energy of the optimal structure folded by the segment, Ef is the optimal free energy in which all previous base-pairs formed in the original optimal structure are prohibited, Ediff(w) and stdw are the sample mean and standard deviation, respectively, of the Ediff scores computed by sliding a fixed-length window in steps of a few nucleotides from 5' to 3' along the searched sequence.
Consequently, the measures Zscre and/or Ediff signify the stability and uniqueness of the predicted RNA secondary structure from the local segment. The greater the Zscre and/or Ediff of the segment are, the more well-ordered the folded RNA structure is expected to be. The program is based on the dynamic programming algorithm and implemented in Fortran 90 running on Unix.
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