Arrays containing values of mutual information for single residues (HEC_MI1) and pairs of residues (HEC_MI2) located within 10 residues of the position being predicted (position "0"). The arrays have dimensions corresponding to the 20 (standard) amino acids, positions (-10 to 10), and states (helix ("H"), sheet ("E"), or coil ("C")).
A character vector of common restriction sites named by the restriction enzyme that cuts at each site. Sequence specificity is listed in 5' to 3' orientation based on the IUPAC_CODE_MAP. The cut site is either signified by a “/” for palindromic sites, or two numbers giving the position of the top and bottom cut positions relative to the site's 3'-end.
An 8D array with four adjacent base pairs of the probe and target sequences at a time. Each dimension has five elements defining the residue at that position ("A", "C", "G", "T", or "-"). The array contains the standard Gibbs free energy change of probe binding (dG, [kcal/mol]) for every quadruple base pairing.
An 8D array with four adjacent base pairs of the primer and target sequences at a time. Each dimension has five elements defining the residue at that position ("A", "C", "G", "T", or "-"). The array contains the standard enthalpy change of probe binding (dH, [kcal/mol]) for every quadruple base pairing.
An 8D array with four adjacent base pairs of the primer and target sequences at a time. Each dimension has five elements defining the residue at that position ("A", "C", "G", "T", or "-"). The array contains the standard entropy change of probe binding (dS, [kcal/mol]) for every quadruple base pairing.
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