tm_nn: Calculate melting temperature using nearest neighbor...
In TmCalculator: Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration
tm_nn R Documentation
Calculate melting temperature using nearest neighbor thermodynamics
Description
Calculates melting temperature (Tm) from nearest-neighbor (NN) thermodynamics,
summing the stacking enthalpies and entropies of adjacent base-pair steps and
applying initiation, symmetry, salt and chemical corrections. Terminal
mismatches, internal mismatches and dangling ends are supported through
dedicated parameter tables. The function verifies that every dinucleotide step
in the input sequence is present in the selected tables before calculating.
Usage
tm_nn(
gr_seq,
ambiguous = FALSE,
shift = 0,
nn_table = c("DNA_NN_SantaLucia_2004", "DNA_NN_Breslauer_1986", "DNA_NN_Sugimoto_1996",
"DNA_NN_Allawi_1998", "RNA_NN_Freier_1986", "RNA_NN_Xia_1998", "RNA_NN_Chen_2012",
"RNA_DNA_NN_Sugimoto_1995", "DNA_NN_Weber_2015", "DNA_NN_Weber_OW04_69",
"DNA_NN_Weber_OW04_119", "DNA_NN_Weber_OW04_220", "DNA_NN_Weber_OW04_621",
"DNA_NN_Weber_OW04_1020", "RNA_NN_Weber_VIF_71", "RNA_NN_Weber_VIF_121",
"RNA_NN_Weber_VIF_221", "RNA_NN_Weber_VIF_621", "RNA_NN_Weber_VIF_1021",
"RNA_NN_Weber_FIF_71", "RNA_NN_Weber_FIF_121",
"RNA_NN_Weber_FIF_221",
"RNA_NN_Weber_FIF_621", "RNA_NN_Weber_FIF_1021", "RNA_DNA_NN_Weber_2019_FT",
"RNA_DNA_NN_Weber_2019_VH", "RNA_DNA_NN_Weber_2019_LS"),
tmm_table = "DNA_TMM_Bommarito_2000",
imm_table = "DNA_IMM_Peyret_1999",
de_table = c("DNA_DE_Bommarito_2000", "RNA_DE_Turner_2010"),
dnac_high = 25,
dnac_low = 25,
self_comp = FALSE,
Na = 50,
K = 0,
Tris = 0,
Mg = 0,
dNTPs = 0,
salt_method = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
"Owczarzy2004", "Owczarzy2008", "none"),
DMSO = 0,
formamide_unit = list(value = 0, unit = "percent"),
dmso_factor = 0.75,
formamide_factor = 0.65
)
Arguments
gr_seq
Pre-processed sequence(s) in 5' to 3' direction. This should be the output from
to_genomic_ranges() function.
ambiguous
Logical value controlling how ambiguous bases are handled:
- TRUE: Ambiguous bases (e.g., N, R, Y) are included in calculations
- FALSE (default): Ambiguous bases are excluded from calculations
shift
Integer value controlling the alignment offset between primer and template sequences.
Visual representation of different shift values:
shift = 0 (default):
Primer: 5' ATGCG 3'
Template: 3' TACGC 5'
shift = -1:
Primer: 5' ATGCG 3'
Template: 3' TACGC 5'
^
shift = 1:
Primer: 5' ATGCG 3'
Template: 3' TACGC 5'
^
The shift parameter is necessary when:
- Sequences have different lengths
- Dangling ends are required
- Specific alignment positions are needed
nn_table
Thermodynamic nearest-neighbor parameters for different nucleic acid hybridizations.
Twenty-seven parameter sets are available, organized by hybridization type.
Sets marked with a sodium concentration were fitted at that condition and
are not salt-corrected further (see the "Choosing a parameter set" section).
DNA/DNA hybridizations, reference salt:
- "DNA_NN_Breslauer_1986": Original DNA/DNA parameters
- "DNA_NN_Sugimoto_1996": Improved DNA/DNA parameters
- "DNA_NN_Allawi_1998": DNA/DNA parameters with internal mismatch corrections
- "DNA_NN_SantaLucia_2004": Unified DNA/DNA parameters (default)
DNA/DNA hybridizations, melting-temperature optimized (Weber 2015):
- "DNA_NN_Weber_2015": Combined dataset, 1020 mM. Recommended when a
salt-optimized DNA set is wanted at high salt
- "DNA_NN_Weber_OW04_69", "...119", "...220", "...621", "...1020":
fitted independently at 69, 119, 220, 621 and 1020 mM sodium
RNA/RNA hybridizations, reference salt:
- "RNA_NN_Freier_1986": Original RNA/RNA parameters
- "RNA_NN_Xia_1998": Improved RNA/RNA parameters
- "RNA_NN_Chen_2012": Updated RNA/RNA parameters with GU pair corrections
RNA/RNA hybridizations, salt-optimized (Ferreira 2019). VIF (variable
initiation factors) gave better cross-validation than FIF (fixed):
- "RNA_NN_Weber_VIF_71", "...121", "...221", "...621", "...1021"
- "RNA_NN_Weber_FIF_71", "...121", "...221", "...621", "...1021"
RNA/DNA hybridizations:
- "RNA_DNA_NN_Sugimoto_1995": RNA/DNA hybridization parameters
- "RNA_DNA_NN_Weber_2019_FT": curve-fitting derived, 1000 mM. Best
performing high-salt hybrid set in Basilio Barbosa (2019)
- "RNA_DNA_NN_Weber_2019_VH": van't Hoff derived, 1000 mM
- "RNA_DNA_NN_Weber_2019_LS": low salt, 100 mM
tmm_table
Thermodynamic parameters for terminal mismatches. Default: "DNA_TMM_Bommarito_2000"
These parameters account for mismatches at the ends of the duplex.
imm_table
Thermodynamic parameters for internal mismatches. Default: "DNA_IMM_Peyret_1999"
These parameters account for mismatches within the duplex, including inosine mismatches.
de_table
Thermodynamic parameters for dangling ends. Default: "DNA_DE_Bommarito_2000"
Available options:
- "DNA_DE_Bommarito_2000": Parameters for DNA dangling ends
- "RNA_DE_Turner_2010": Parameters for RNA dangling ends
dnac_high
Concentration of the higher concentrated strand in nM. Default: 25
Typically this is the primer (for PCR) or the probe concentration.
dnac_low
Concentration of the lower concentrated strand in nM. Default: 25
This is typically the template concentration.
self_comp
Logical value indicating if the sequence is self-complementary:
- TRUE: Sequence can bind to itself, dnac_low is ignored
- FALSE (default): Sequence binds to a different complementary sequence
Na
Millimolar concentration of sodium ions. Default: 50
K
Millimolar concentration of potassium ions. Default: 0
Tris
Millimolar concentration of Tris buffer. Default: 0
Mg
Millimolar concentration of magnesium ions. Default: 0
dNTPs
Millimolar concentration of deoxynucleotide triphosphates. Default: 0
salt_method
Salt correction method. Options are:
Available options:
- "Schildkraut2010": Updated salt correction method
- "Wetmur1991": Classic salt correction method
- "SantaLucia1996": DNA-specific salt correction
- "SantaLucia1998-1": Improved DNA salt correction
- "Owczarzy2004": Comprehensive salt correction
- "Owczarzy2008": Updated comprehensive salt correction
- "none": Disables salt correction entirely
Note: Parameter sets fitted at a specific sodium concentration (those
carrying a "salt_mM" attribute, i.e. the Weber/VarGibbs series) already
account for salt. When the requested Na matches the concentration
such a set was fitted at, salt correction is skipped automatically; when
it does not, a warning is issued.
DMSO
Percent DMSO concentration in the reaction mixture. Default: 0
DMSO can lower the melting temperature of nucleic acid duplexes.
formamide_unit
Formamide concentration as 'list(value, unit)'. Default: list(value = 0, unit = "percent")
- value: numeric value of formamide concentration
- unit: character string specifying the unit ("percent" or "molar")
Default: list(value=0, unit="percent")
dmso_factor
Coefficient of melting temperature (Tm) decrease per percent DMSO.
Default: 0.75 (von Ahsen N, 2001, PMID:11673362)
Other published values: 0.5, 0.6, 0.675
formamide_factor
Coefficient of melting temperature (Tm) decrease per percent formamide.
Default: 0.65
Literature reports values ranging from 0.6 to 0.72
Details
DNA_NN_Breslauer_1986: Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>
DNA_NN_Sugimoto_1996: Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>
DNA_NN_Allawi_1998: Allawi H (1998) <doi:10.1093/nar/26.11.2694>
DNA_NN_SantaLucia_2004: SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>
RNA_NN_Freier_1986: Freier S (1986) <doi:10.1073/pnas.83.24.9373>
RNA_NN_Xia_1998: Xia T (1998) <doi:10.1021/bi9809425>
RNA_NN_Chen_2012: Chen JL (2012) <doi:10.1021/bi3002709>
RNA_DNA_NN_Sugimoto_1995: Sugimoto N (1995)<doi:10.1016/S0048-9697(98)00088-6>
The following sets were derived by melting-temperature optimization and are
fitted at the sodium concentration given in parentheses. They are not
salt-corrected further; see the “Choosing a parameter set” section.
DNA_NN_Weber_2015 (1020 mM): Weber G (2015) <doi:10.1093/bioinformatics/btu751>
DNA_NN_Weber_OW04_69 (69 mM), DNA_NN_Weber_OW04_119 (119 mM),
DNA_NN_Weber_OW04_220 (220 mM), DNA_NN_Weber_OW04_621 (621 mM),
DNA_NN_Weber_OW04_1020 (1020 mM): Weber G (2015) <doi:10.1093/bioinformatics/btu751>
RNA_NN_Weber_VIF_71 (71 mM), RNA_NN_Weber_VIF_121 (121 mM),
RNA_NN_Weber_VIF_221 (221 mM), RNA_NN_Weber_VIF_621 (621 mM),
RNA_NN_Weber_VIF_1021 (1021 mM): Ferreira I (2019) <doi:10.1016/j.chemphys.2019.01.016>,
variable initiation factors
RNA_NN_Weber_FIF_71 (71 mM), RNA_NN_Weber_FIF_121 (121 mM),
RNA_NN_Weber_FIF_221 (221 mM), RNA_NN_Weber_FIF_621 (621 mM),
RNA_NN_Weber_FIF_1021 (1021 mM): Ferreira I (2019) <doi:10.1016/j.chemphys.2019.01.016>,
fixed initiation factors
RNA_DNA_NN_Weber_2019_FT (1000 mM), RNA_DNA_NN_Weber_2019_VH (1000 mM),
RNA_DNA_NN_Weber_2019_LS (100 mM): Basilio Barbosa V (2019) <doi:10.1016/j.bpc.2019.106189>
DNA_TMM_Bommarito_2000: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>
DNA_IMM_Peyret_1999: Peyret N (1999) <doi:10.1021/bi9825091> & Allawi H T (1997) <doi:10.1021/bi962590c> & Santalucia N (2005) <doi:10.1093/nar/gki918>
DNA_DE_Bommarito_2000: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>
RNA_DE_Turner_2010: Turner D H (2010) <doi:10.1093/nar/gkp892>
Value
A TmCalculator list with:
gr
The input GRanges with metadata columns Tm
and GC (melting temperature in ^{\circ}C and GC percent).
Sequences that could not be evaluated receive NA.
options
The calculation parameters actually used, including
the parameter tables and their citations, ion and additive
concentrations, Salt correction method, and two fields recording
how salt was handled: Salt correction applied (logical) and
Parameter set fitted at [Na+] (mM), which is NA for
reference-salt sets. Regions skipped for containing N are listed
in Skipped regions containing N.
Choosing a parameter set
Parameter sets fall into two families that are handled differently.
Reference-salt sets (Breslauer 1986, Sugimoto 1996, Allawi 1998,
SantaLucia 2004, Freier 1986, Xia 1998, Chen 2012, Sugimoto 1995) were fitted
at a single reference sodium concentration, and other conditions are reached
by applying one of the salt_method correction formulas.
Condition-specific sets (the Weber/VarGibbs series) were instead
fitted directly at a stated sodium concentration and are intended to
replace salt correction rather than be corrected. Each carries a
salt_mM attribute. When the requested Na matches that value,
salt correction is skipped automatically; when it does not, the correction is
still applied but a warning is issued, since correcting an already
condition-specific set double-counts the ionic effect. Whether a correction
was applied is recorded in the returned options.
As a rule of thumb, pick the set whose fitted salt is closest to your
experimental condition rather than correcting a distant one.
Author(s)
Junhui Li
References
Breslauer K J , Frank R , Blocker H , et al. Predicting DNA duplex stability from the base sequence.[J]. Proceedings of the National Academy of Sciences, 1986, 83(11):3746-3750.
Sugimoto N , Nakano S , Yoneyama M , et al. Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes[J]. Nucleic Acids Research, 1996, 24(22):4501-5.
Allawi, H. Thermodynamics of internal C.T mismatches in DNA[J]. Nucleic Acids Research, 1998, 26(11):2694-2701.
Hicks L D , Santalucia J . The thermodynamics of DNA structural motifs.[J]. Annual Review of Biophysics & Biomolecular Structure, 2004, 33(1):415-440.
Freier S M , Kierzek R , Jaeger J A , et al. Improved free-energy parameters for predictions of RNA duplex stability.[J]. Proceedings of the National Academy of Sciences, 1986, 83(24):9373-9377.
Xia T , Santalucia , J , Burkard M E , et al. Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs,[J]. Biochemistry, 1998, 37(42):14719-14735.
Chen J L , Dishler A L , Kennedy S D , et al. Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters[J]. Biochemistry, 2012, 51(16):3508-3522.
Bommarito S, Peyret N, Jr S L. Thermodynamic parameters for DNA sequences with dangling ends[J]. Nucleic Acids Research, 2000, 28(9):1929-1934.
Turner D H , Mathews D H . NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure[J]. Nucleic Acids Research, 2010, 38(Database issue):D280-D282.
Sugimoto N , Nakano S I , Katoh M , et al. Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes[J]. Biochemistry, 1995, 34(35):11211-11216.
Allawi H, SantaLucia J: Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 1997, 36:10581-10594.
Santalucia N E W J . Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes[J]. Nucleic Acids Research, 2005, 33(19):6258-67.
Peyret N , Seneviratne P A , Allawi H T , et al. Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches, [J]. Biochemistry, 1999, 38(12):3468-3477.
Weber G. Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures[J]. Bioinformatics, 2015, 31(6):871-877.
Ferreira I, Jolley E A, Znosko B M, et al. Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters[J]. Chemical Physics, 2019, 521:69-76.
Basilio Barbosa V, de Oliveira Martins E, Weber G. Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations[J]. Biophysical Chemistry, 2019, 251:106189.
See Also
tm_calculate for a single entry point to the
nearest-neighbor, GC-content and Wallace methods.
Examples
input_seq <- c("AAAATTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGTGTGCGCTGC",
"AAAATTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGTGTGCGCTGC")
seqs <- to_genomic_ranges(input_seq)
out <- tm_nn(seqs, Na=50)
out
# A parameter set fitted at a stated sodium concentration. Because Na
# matches the concentration the set was fitted at, salt correction is
# skipped automatically rather than applied on top of it.
out_ls <- tm_nn(seqs, nn_table = "RNA_DNA_NN_Weber_2019_LS", Na = 100)
out_ls$options[["Salt correction applied"]]
out_ls$options[["Parameter set fitted at [Na+] (mM)"]]
TmCalculator documentation built on Aug. 28, 2026, 5:09 p.m.
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| tm_nn | R Documentation |
Calculate melting temperature using nearest neighbor thermodynamics
Description
Calculates melting temperature (Tm) from nearest-neighbor (NN) thermodynamics, summing the stacking enthalpies and entropies of adjacent base-pair steps and applying initiation, symmetry, salt and chemical corrections. Terminal mismatches, internal mismatches and dangling ends are supported through dedicated parameter tables. The function verifies that every dinucleotide step in the input sequence is present in the selected tables before calculating.
Usage
tm_nn(
gr_seq,
ambiguous = FALSE,
shift = 0,
nn_table = c("DNA_NN_SantaLucia_2004", "DNA_NN_Breslauer_1986", "DNA_NN_Sugimoto_1996",
"DNA_NN_Allawi_1998", "RNA_NN_Freier_1986", "RNA_NN_Xia_1998", "RNA_NN_Chen_2012",
"RNA_DNA_NN_Sugimoto_1995", "DNA_NN_Weber_2015", "DNA_NN_Weber_OW04_69",
"DNA_NN_Weber_OW04_119", "DNA_NN_Weber_OW04_220", "DNA_NN_Weber_OW04_621",
"DNA_NN_Weber_OW04_1020", "RNA_NN_Weber_VIF_71", "RNA_NN_Weber_VIF_121",
"RNA_NN_Weber_VIF_221", "RNA_NN_Weber_VIF_621", "RNA_NN_Weber_VIF_1021",
"RNA_NN_Weber_FIF_71", "RNA_NN_Weber_FIF_121",
"RNA_NN_Weber_FIF_221",
"RNA_NN_Weber_FIF_621", "RNA_NN_Weber_FIF_1021", "RNA_DNA_NN_Weber_2019_FT",
"RNA_DNA_NN_Weber_2019_VH", "RNA_DNA_NN_Weber_2019_LS"),
tmm_table = "DNA_TMM_Bommarito_2000",
imm_table = "DNA_IMM_Peyret_1999",
de_table = c("DNA_DE_Bommarito_2000", "RNA_DE_Turner_2010"),
dnac_high = 25,
dnac_low = 25,
self_comp = FALSE,
Na = 50,
K = 0,
Tris = 0,
Mg = 0,
dNTPs = 0,
salt_method = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
"Owczarzy2004", "Owczarzy2008", "none"),
DMSO = 0,
formamide_unit = list(value = 0, unit = "percent"),
dmso_factor = 0.75,
formamide_factor = 0.65
)
Arguments
gr_seq |
Pre-processed sequence(s) in 5' to 3' direction. This should be the output from to_genomic_ranges() function. |
ambiguous |
Logical value controlling how ambiguous bases are handled: - TRUE: Ambiguous bases (e.g., N, R, Y) are included in calculations - FALSE (default): Ambiguous bases are excluded from calculations |
shift |
Integer value controlling the alignment offset between primer and template sequences. Visual representation of different shift values: shift = 0 (default): Primer: 5' ATGCG 3' Template: 3' TACGC 5' shift = -1: Primer: 5' ATGCG 3' Template: 3' TACGC 5' ^ shift = 1: Primer: 5' ATGCG 3' Template: 3' TACGC 5' ^ The shift parameter is necessary when: - Sequences have different lengths - Dangling ends are required - Specific alignment positions are needed |
nn_table |
Thermodynamic nearest-neighbor parameters for different nucleic acid hybridizations. Twenty-seven parameter sets are available, organized by hybridization type. Sets marked with a sodium concentration were fitted at that condition and are not salt-corrected further (see the "Choosing a parameter set" section). DNA/DNA hybridizations, reference salt: - "DNA_NN_Breslauer_1986": Original DNA/DNA parameters - "DNA_NN_Sugimoto_1996": Improved DNA/DNA parameters - "DNA_NN_Allawi_1998": DNA/DNA parameters with internal mismatch corrections - "DNA_NN_SantaLucia_2004": Unified DNA/DNA parameters (default) DNA/DNA hybridizations, melting-temperature optimized (Weber 2015): - "DNA_NN_Weber_2015": Combined dataset, 1020 mM. Recommended when a salt-optimized DNA set is wanted at high salt - "DNA_NN_Weber_OW04_69", "...119", "...220", "...621", "...1020": fitted independently at 69, 119, 220, 621 and 1020 mM sodium RNA/RNA hybridizations, reference salt: - "RNA_NN_Freier_1986": Original RNA/RNA parameters - "RNA_NN_Xia_1998": Improved RNA/RNA parameters - "RNA_NN_Chen_2012": Updated RNA/RNA parameters with GU pair corrections RNA/RNA hybridizations, salt-optimized (Ferreira 2019). VIF (variable initiation factors) gave better cross-validation than FIF (fixed): - "RNA_NN_Weber_VIF_71", "...121", "...221", "...621", "...1021" - "RNA_NN_Weber_FIF_71", "...121", "...221", "...621", "...1021" RNA/DNA hybridizations: - "RNA_DNA_NN_Sugimoto_1995": RNA/DNA hybridization parameters - "RNA_DNA_NN_Weber_2019_FT": curve-fitting derived, 1000 mM. Best performing high-salt hybrid set in Basilio Barbosa (2019) - "RNA_DNA_NN_Weber_2019_VH": van't Hoff derived, 1000 mM - "RNA_DNA_NN_Weber_2019_LS": low salt, 100 mM |
tmm_table |
Thermodynamic parameters for terminal mismatches. Default: "DNA_TMM_Bommarito_2000" These parameters account for mismatches at the ends of the duplex. |
imm_table |
Thermodynamic parameters for internal mismatches. Default: "DNA_IMM_Peyret_1999" These parameters account for mismatches within the duplex, including inosine mismatches. |
de_table |
Thermodynamic parameters for dangling ends. Default: "DNA_DE_Bommarito_2000" Available options: - "DNA_DE_Bommarito_2000": Parameters for DNA dangling ends - "RNA_DE_Turner_2010": Parameters for RNA dangling ends |
dnac_high |
Concentration of the higher concentrated strand in nM. Default: 25 Typically this is the primer (for PCR) or the probe concentration. |
dnac_low |
Concentration of the lower concentrated strand in nM. Default: 25 This is typically the template concentration. |
self_comp |
Logical value indicating if the sequence is self-complementary: - TRUE: Sequence can bind to itself, dnac_low is ignored - FALSE (default): Sequence binds to a different complementary sequence |
Na |
Millimolar concentration of sodium ions. Default: 50 |
K |
Millimolar concentration of potassium ions. Default: 0 |
Tris |
Millimolar concentration of Tris buffer. Default: 0 |
Mg |
Millimolar concentration of magnesium ions. Default: 0 |
dNTPs |
Millimolar concentration of deoxynucleotide triphosphates. Default: 0 |
salt_method |
Salt correction method. Options are:
Available options:
- "Schildkraut2010": Updated salt correction method
- "Wetmur1991": Classic salt correction method
- "SantaLucia1996": DNA-specific salt correction
- "SantaLucia1998-1": Improved DNA salt correction
- "Owczarzy2004": Comprehensive salt correction
- "Owczarzy2008": Updated comprehensive salt correction
- "none": Disables salt correction entirely
Note: Parameter sets fitted at a specific sodium concentration (those
carrying a "salt_mM" attribute, i.e. the Weber/VarGibbs series) already
account for salt. When the requested |
DMSO |
Percent DMSO concentration in the reaction mixture. Default: 0 DMSO can lower the melting temperature of nucleic acid duplexes. |
formamide_unit |
Formamide concentration as 'list(value, unit)'. Default: list(value = 0, unit = "percent") - value: numeric value of formamide concentration - unit: character string specifying the unit ("percent" or "molar") Default: list(value=0, unit="percent") |
dmso_factor |
Coefficient of melting temperature (Tm) decrease per percent DMSO. Default: 0.75 (von Ahsen N, 2001, PMID:11673362) Other published values: 0.5, 0.6, 0.675 |
formamide_factor |
Coefficient of melting temperature (Tm) decrease per percent formamide. Default: 0.65 Literature reports values ranging from 0.6 to 0.72 |
Details
DNA_NN_Breslauer_1986: Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>
DNA_NN_Sugimoto_1996: Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>
DNA_NN_Allawi_1998: Allawi H (1998) <doi:10.1093/nar/26.11.2694>
DNA_NN_SantaLucia_2004: SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>
RNA_NN_Freier_1986: Freier S (1986) <doi:10.1073/pnas.83.24.9373>
RNA_NN_Xia_1998: Xia T (1998) <doi:10.1021/bi9809425>
RNA_NN_Chen_2012: Chen JL (2012) <doi:10.1021/bi3002709>
RNA_DNA_NN_Sugimoto_1995: Sugimoto N (1995)<doi:10.1016/S0048-9697(98)00088-6>
The following sets were derived by melting-temperature optimization and are fitted at the sodium concentration given in parentheses. They are not salt-corrected further; see the “Choosing a parameter set” section.
DNA_NN_Weber_2015 (1020 mM): Weber G (2015) <doi:10.1093/bioinformatics/btu751>
DNA_NN_Weber_OW04_69 (69 mM), DNA_NN_Weber_OW04_119 (119 mM), DNA_NN_Weber_OW04_220 (220 mM), DNA_NN_Weber_OW04_621 (621 mM), DNA_NN_Weber_OW04_1020 (1020 mM): Weber G (2015) <doi:10.1093/bioinformatics/btu751>
RNA_NN_Weber_VIF_71 (71 mM), RNA_NN_Weber_VIF_121 (121 mM), RNA_NN_Weber_VIF_221 (221 mM), RNA_NN_Weber_VIF_621 (621 mM), RNA_NN_Weber_VIF_1021 (1021 mM): Ferreira I (2019) <doi:10.1016/j.chemphys.2019.01.016>, variable initiation factors
RNA_NN_Weber_FIF_71 (71 mM), RNA_NN_Weber_FIF_121 (121 mM), RNA_NN_Weber_FIF_221 (221 mM), RNA_NN_Weber_FIF_621 (621 mM), RNA_NN_Weber_FIF_1021 (1021 mM): Ferreira I (2019) <doi:10.1016/j.chemphys.2019.01.016>, fixed initiation factors
RNA_DNA_NN_Weber_2019_FT (1000 mM), RNA_DNA_NN_Weber_2019_VH (1000 mM), RNA_DNA_NN_Weber_2019_LS (100 mM): Basilio Barbosa V (2019) <doi:10.1016/j.bpc.2019.106189>
DNA_TMM_Bommarito_2000: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>
DNA_IMM_Peyret_1999: Peyret N (1999) <doi:10.1021/bi9825091> & Allawi H T (1997) <doi:10.1021/bi962590c> & Santalucia N (2005) <doi:10.1093/nar/gki918>
DNA_DE_Bommarito_2000: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>
RNA_DE_Turner_2010: Turner D H (2010) <doi:10.1093/nar/gkp892>
Value
A TmCalculator list with:
gr |
The input |
options |
The calculation parameters actually used, including
the parameter tables and their citations, ion and additive
concentrations, |
Choosing a parameter set
Parameter sets fall into two families that are handled differently.
Reference-salt sets (Breslauer 1986, Sugimoto 1996, Allawi 1998,
SantaLucia 2004, Freier 1986, Xia 1998, Chen 2012, Sugimoto 1995) were fitted
at a single reference sodium concentration, and other conditions are reached
by applying one of the salt_method correction formulas.
Condition-specific sets (the Weber/VarGibbs series) were instead
fitted directly at a stated sodium concentration and are intended to
replace salt correction rather than be corrected. Each carries a
salt_mM attribute. When the requested Na matches that value,
salt correction is skipped automatically; when it does not, the correction is
still applied but a warning is issued, since correcting an already
condition-specific set double-counts the ionic effect. Whether a correction
was applied is recorded in the returned options.
As a rule of thumb, pick the set whose fitted salt is closest to your experimental condition rather than correcting a distant one.
Author(s)
Junhui Li
References
Breslauer K J , Frank R , Blocker H , et al. Predicting DNA duplex stability from the base sequence.[J]. Proceedings of the National Academy of Sciences, 1986, 83(11):3746-3750.
Sugimoto N , Nakano S , Yoneyama M , et al. Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes[J]. Nucleic Acids Research, 1996, 24(22):4501-5.
Allawi, H. Thermodynamics of internal C.T mismatches in DNA[J]. Nucleic Acids Research, 1998, 26(11):2694-2701.
Hicks L D , Santalucia J . The thermodynamics of DNA structural motifs.[J]. Annual Review of Biophysics & Biomolecular Structure, 2004, 33(1):415-440.
Freier S M , Kierzek R , Jaeger J A , et al. Improved free-energy parameters for predictions of RNA duplex stability.[J]. Proceedings of the National Academy of Sciences, 1986, 83(24):9373-9377.
Xia T , Santalucia , J , Burkard M E , et al. Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs,[J]. Biochemistry, 1998, 37(42):14719-14735.
Chen J L , Dishler A L , Kennedy S D , et al. Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters[J]. Biochemistry, 2012, 51(16):3508-3522.
Bommarito S, Peyret N, Jr S L. Thermodynamic parameters for DNA sequences with dangling ends[J]. Nucleic Acids Research, 2000, 28(9):1929-1934.
Turner D H , Mathews D H . NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure[J]. Nucleic Acids Research, 2010, 38(Database issue):D280-D282.
Sugimoto N , Nakano S I , Katoh M , et al. Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes[J]. Biochemistry, 1995, 34(35):11211-11216.
Allawi H, SantaLucia J: Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry 1997, 36:10581-10594.
Santalucia N E W J . Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes[J]. Nucleic Acids Research, 2005, 33(19):6258-67.
Peyret N , Seneviratne P A , Allawi H T , et al. Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches, [J]. Biochemistry, 1999, 38(12):3468-3477.
Weber G. Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures[J]. Bioinformatics, 2015, 31(6):871-877.
Ferreira I, Jolley E A, Znosko B M, et al. Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters[J]. Chemical Physics, 2019, 521:69-76.
Basilio Barbosa V, de Oliveira Martins E, Weber G. Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations[J]. Biophysical Chemistry, 2019, 251:106189.
See Also
tm_calculate for a single entry point to the
nearest-neighbor, GC-content and Wallace methods.
Examples
input_seq <- c("AAAATTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGTGTGCGCTGC",
"AAAATTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGTGTGCGCTGC")
seqs <- to_genomic_ranges(input_seq)
out <- tm_nn(seqs, Na=50)
out
# A parameter set fitted at a stated sodium concentration. Because Na
# matches the concentration the set was fitted at, salt correction is
# skipped automatically rather than applied on top of it.
out_ls <- tm_nn(seqs, nn_table = "RNA_DNA_NN_Weber_2019_LS", Na = 100)
out_ls$options[["Salt correction applied"]]
out_ls$options[["Parameter set fitted at [Na+] (mM)"]]
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