TmCalculator 1.0.9

Bug fixes

• Corrected two entropy values in DNA_NN_SantaLucia_2004. The TA/AT step was -20.4 (duplicated from the adjacent AT/TA row) and should be -21.3; the GG/CC step was -19.0 and should be -19.9. Both values are shared with DNA_NN_Allawi_1998, which already carried them correctly, so the two tables were internally inconsistent. Tm values computed with DNA_NN_SantaLucia_2004 will change slightly for sequences containing these steps.

New parameter sets

• Added 19 nearest-neighbor parameter sets derived by melting-temperature optimization (Weber and colleagues, UFMG), bringing the total from 8 to 27. Unlike the existing sets, these are fitted directly at a stated sodium concentration and are intended to replace salt correction rather than be corrected.

  • DNA: DNA_NN_Weber_2015 (1020 mM) and a salt series DNA_NN_Weber_OW04_69, _119, _220, _621, _1020.
  • RNA: RNA_NN_Weber_VIF_* and RNA_NN_Weber_FIF_* at 71, 121, 221, 621 and 1021 mM. The VIF (variable initiation factor) sets gave better cross-validation in the source study.
  • RNA/DNA hybrid: RNA_DNA_NN_Weber_2019_FT and _VH (1000 mM) and RNA_DNA_NN_Weber_2019_LS (100 mM).

  Values were taken from the parameter files distributed with VarGibbs 5.0 at full precision rather than transcribed from the published tables. The transcription was validated by confirming that the reference files shipped alongside them reproduce the existing DNA_NN_Allawi_1998, DNA_NN_Sugimoto_1996, RNA_NN_Xia_1998, RNA_NN_Freier_1986 and all 87 rows of DNA_IMM_Peyret_1999 exactly.

Salt handling

• Parameter sets now carry a salt_mM attribute when they were fitted at a specific sodium concentration. tm_nn() uses it to avoid double-counting the ionic contribution:

  • if the requested Na matches the concentration the set was fitted at, salt correction is skipped;
  • if it does not, the correction is applied and a warning names both concentrations.

  Existing parameter sets carry no such attribute, so this is a no-op for all previous usage.

• salt_method gains a "none" option to disable salt correction explicitly. The documentation previously stated that NA would do this, but match.arg() rejected it.

• tm_nn() and tm_calculate() now report Salt correction applied (logical) and Parameter set fitted at [Na+] (mM) in the returned options, so the automatic skip is visible rather than silent.

Documentation

• tm_nn() gained a @return section; the return value was previously undocumented.
• Removed "SantaLucia1998-2" from the documented salt_method options in tm_nn() and tm_calculate(). It was listed in the help pages but absent from the function’s accepted values, so following the documentation produced an error.
• Added a “Choosing a parameter set” section to ?tm_nn and a “Salt handling” section to ?tm_calculate.
• @details for tm_calculate() now explains when each of the three methods is appropriate, including the note that nearest-neighbor parameters are calibrated on short duplexes, so values computed over long sequences or fixed-width genomic windows are best read as a relative measure of local thermodynamic stability rather than as an absolute experimental Tm.
• tm_nn() and tm_calculate() now cross-reference each other via @seealso.