Help for package TmCalculator

Type:

Package

Title:

Melting Temperature of Nucleic Acid Sequences

Version:

1.0.3

Date:

2022-02-20

Author:

Junhui Li

Maintainer:

Junhui Li <junhuili@cau.edu.cn>

Description:

This tool is extended from methods in Bio.SeqUtils.MeltingTemp of python. The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) <doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based on G and C content (Marmur J. (1962) <doi:10.1016/S0022-2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>, Wetmur J G (1991) <doi:10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <doi:10.1093/clinchem/47.11.1956>) and nearest neighbor thermodynamics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>, Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H (1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986) <doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>, Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000) <doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>, Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005) <doi:10.1093/nar/gki918>), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>, SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004) <doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>).

BugReports:

https://github.com/JunhuiLi1017/TmCalculator/issues

License:

GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

Depends:

R (≥ 2.10)

NeedsCompilation:

Repository:

CRAN

RoxygenNote:

7.1.2

Packaged:

2022-02-21 03:44:19 UTC; junhuili

Date/Publication:

2022-02-21 04:10:03 UTC

Calculate G and C content of nucleotide sequences

Description

Calculate G and C content of nucleotide sequences. The number of G and C in sequence is divided by length of sequence(when totalnt is TRUE) or the number of all A,T,C,G and ambiguous base.

Usage

GC(ntseq, ambiguous = FALSE, totalnt = TRUE)

Arguments

ntseq

Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters.

ambiguous

Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.

totalnt

Sum of 'G' and 'C' bases divided by the length of the sequence when totalnt is TRUE.

Value

Content of G and C(range from 0 to 100

Author(s)

Junhui Li

Examples


GC(c("a","t","c","t","g","g","g","c","c","a","g","t","a"))#53.84615
GC("GCATSWSYK",ambiguous = TRUE)#55.55556

Calculate the melting temperature using empirical formulas based on GC content

Description

Calculate the melting temperature using empirical formulas based on GC content with different options

Usage

Tm_GC(
  ntseq,
  ambiguous = FALSE,
  userset = NULL,
  variant = c("Primer3Plus", "Chester1993", "QuikChange", "Schildkraut1965",
    "Wetmur1991_MELTING", "Wetmur1991_RNA", "Wetmur1991_RNA/DNA", "vonAhsen2001"),
  Na = 0,
  K = 0,
  Tris = 0,
  Mg = 0,
  dNTPs = 0,
  saltcorr = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
    "Owczarzy2004", "Owczarzy2008"),
  mismatch = TRUE,
  DMSO = 0,
  fmd = 0,
  DMSOfactor = 0.75,
  fmdfactor = 0.65,
  fmdmethod = c("concentration", "molar"),
  outlist = TRUE
)

Arguments

ntseq

Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters.

ambiguous

Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.

userset

A vector of four coefficient values. Usersets override value sets.

variant

Empirical constants coefficient with 8 variant: Chester1993, QuikChange, Schildkraut1965, Wetmur1991_MELTING, Wetmur1991_RNA, Wetmur1991_RNA/DNA, Primer3Plus and vonAhsen2001

Na

Millimolar concentration of Na, default is 0

K

Millimolar concentration of K, default is 0

Tris

Millimolar concentration of Tris, default is 0

Mg

Millimolar concentration of Mg, default is 0

dNTPs

Millimolar concentration of dNTPs, default is 0

saltcorr

Salt correction method should be chosen when provide 'userset'. Options are "Schildkraut2010", "Wetmur1991","SantaLucia1996","SantaLucia1998-1","Owczarzy2004","Owczarzy2008". Note that "SantaLucia1998-2" is not available for this function.

mismatch

If 'True' (default) every 'X' in the sequence is counted as mismatch

DMSO

Percent DMSO

fmd

Formamide concentration in percentage (fmdmethod="concentration") or molar (fmdmethod="molar").

DMSOfactor

Coeffecient of Tm decreases per percent DMSO. Default=0.75 von Ahsen N (2001) <PMID:11673362>. Other published values are 0.5, 0.6 and 0.675.

fmdfactor

Coeffecient of Tm decrease per percent formamide. Default=0.65. Several papers report factors between 0.6 and 0.72.

fmdmethod

"concentration" method for formamide concentration in percentage and "molar" for formamide concentration in molar

outlist

output a list of Tm and options or only Tm value, default is TRUE.

Details

Empirical constants coefficient with 8 variant:

Chester1993: Tm = 69.3 + 0.41(Percentage_GC) - 650/N

QuikChange: Tm = 81.5 + 0.41(Percentage_GC) - 675/N - Percentage_mismatch

Schildkraut1965: Tm = 81.5 + 0.41(Percentage_GC) - 675/N + 16.6 x log[Na+]

Wetmur1991_MELTING: Tm = 81.5 + 0.41(Percentage_GC) - 500/N + 16.6 x log([Na+]/(1.0 + 0.7 x [Na+])) - Percentage_mismatch

Wetmur1991_RNA: Tm = 78 + 0.7(Percentage_GC) - 500/N + 16.6 x log([Na+]/(1.0 + 0.7 x [Na+])) - Percentage_mismatch

Wetmur1991_RNA/DNA: Tm = 67 + 0.8(Percentage_GC) - 500/N + 16.6 x log([Na+]/(1.0 + 0.7 x [Na+])) - Percentage_mismatch

Primer3Plus: Tm = 81.5 + 0.41(Percentage_GC) - 600/N + 16.6 x log[Na+]

vonAhsen2001: Tm = 77.1 + 0.41(Percentage_GC) - 528/N + 11.7 x log[Na+]

Author(s)

Junhui Li

References

Marmur J , Doty P . Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature.[J]. Journal of Molecular Biology, 1962, 5(1):109-118.

Schildkraut C . Dependence of the melting temperature of DNA on salt concentration[J]. Biopolymers, 2010, 3(2):195-208.

Wetmur J G . DNA Probes: Applications of the Principles of Nucleic Acid Hybridization[J]. CRC Critical Reviews in Biochemistry, 1991, 26(3-4):33.

Untergasser A , Cutcutache I , Koressaar T , et al. Primer3–new capabilities and interfaces[J]. Nucleic Acids Research, 2012, 40(15):e115-e115.

von Ahsen N, Wittwer CT, Schutz E , et al. Oligonucleotide melting temperatures under PCR conditions: deoxynucleotide Triphosphate and Dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin Chem 2001, 47:1956-1961.

Examples


ntseq <- c("ATCGTGCGTAGCAGTACGATCAGTAG")
out <- Tm_GC(ntseq,ambiguous=TRUE,variant="Primer3Plus",Na=50,mismatch=TRUE)
out
out$Tm
out$Options

Calculate melting temperature using nearest neighbor thermodynamics

Description

Calculate melting temperature using nearest neighbor thermodynamics

Usage

Tm_NN(
  ntseq,
  ambiguous = FALSE,
  comSeq = NULL,
  shift = 0,
  nn_table = c("DNA_NN4", "DNA_NN1", "DNA_NN2", "DNA_NN3", "RNA_NN1", "RNA_NN2",
    "RNA_NN3", "R_DNA_NN1"),
  tmm_table = "DNA_TMM1",
  imm_table = "DNA_IMM1",
  de_table = c("DNA_DE1", "RNA_DE1"),
  dnac1 = 25,
  dnac2 = 25,
  selfcomp = FALSE,
  Na = 0,
  K = 0,
  Tris = 0,
  Mg = 0,
  dNTPs = 0,
  saltcorr = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
    "SantaLucia1998-2", "Owczarzy2004", "Owczarzy2008"),
  DMSO = 0,
  fmd = 0,
  DMSOfactor = 0.75,
  fmdfactor = 0.65,
  fmdmethod = c("concentration", "molar"),
  outlist = TRUE
)

Arguments

ntseq

Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters.

ambiguous

Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.Default is FALSE.

comSeq

Complementary sequence. The sequence of the template/target in 3'->5' direction

shift

Shift of the primer/probe sequence on the template/target sequence, default=0. for example: when shift=0, the first nucleotide base at 5' end of primer align to first one at 3' end of template. When shift=-1, the second nucleotide base at 5' end of primer align to first one at 3' end of template.

When shift=1, the first nucleotide base at 5' end of primer align to second one at 3' end of template. The shift parameter is necessary to align primer/probe and template/target if they have different lengths or if they should have dangling ends.

nn_table

Thermodynamic NN values, eight tables are implemented.

For DNA/DNA hybridizations: DNA_NN1,DNA_NN2,DNA_NN3,DNA_NN4

For RNA/RNA hybridizations: RNA_NN1,RNA_NN2,RNA_NN3

For RNA/DNA hybridizations: R_DNA_NN1

tmm_table

Thermodynamic values for terminal mismatches. Default: DNA_TMM1

imm_table

Thermodynamic values for internal mismatches, may include insosine mismatches. Default: DNA_IMM1

de_table

Thermodynamic values for dangling ends. DNA_DE1(default) and RNA_DE1

dnac1

Concentration of the higher concentrated strand [nM]. Typically this will be the primer (for PCR) or the probe. Default=25.

dnac2

Concentration of the lower concentrated strand [nM].

selfcomp

Sequence self-complementary, default=False. If 'True' the primer is thought binding to itself, thus dnac2 is not considered.

Na

Millimolar concentration of Na, default is 0

K

Millimolar concentration of K, default is 0

Tris

Millimolar concentration of Tris, default is 0

Mg

Millimolar concentration of Mg, default is 0

dNTPs

Millimolar concentration of dNTPs, default is 0

saltcorr

Salt correction method should be chosen when provide 'userset' Options are "Schildkraut2010", "Wetmur1991","SantaLucia1996","SantaLucia1998-1", "SantaLucia1998-2","Owczarzy2004","Owczarzy2008". Note that NA means no salt correction.

DMSO

Percent DMSO

fmd

Formamide concentration in percentage (fmdmethod="concentration") or molar (fmdmethod="molar").

DMSOfactor

Coeffecient of Tm decreases per percent DMSO. Default=0.75 von Ahsen N (2001) <PMID:11673362>. Other published values are 0.5, 0.6 and 0.675.

fmdfactor

Coeffecient of Tm decrease per percent formamide. Default=0.65. Several papers report factors between 0.6 and 0.72.

fmdmethod

"concentration" method for formamide concentration in percentage and "molar" for formamide concentration in molar.

outlist

output a list of Tm and options or only Tm value, default is TRUE.

Details

DNA_NN1: Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>

DNA_NN2: Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>

DNA_NN3: Allawi H (1998) <doi:10.1093/nar/26.11.2694>

DNA_NN4: SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>

RNA_NN1: Freier S (1986) <doi:10.1073/pnas.83.24.9373>

RNA_NN2: Xia T (1998) <doi:10.1021/bi9809425>

RNA_NN3: Chen JL (2012) <doi:10.1021/bi3002709>

R_DNA_NN1: Sugimoto N (1995)<doi:10.1016/S0048-9697(98)00088-6>

DNA_TMM1: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>

DNA_IMM1: Peyret N (1999) <doi:10.1021/bi9825091> & Allawi H T (1997) <doi:10.1021/bi962590c> & Santalucia N (2005) <doi:10.1093/nar/gki918>

DNA_DE1: Bommarito S (2000) <doi:10.1093/nar/28.9.1929>

RNA_DE1: Turner D H (2010) <doi:10.1093/nar/gkp892>

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.

Examples


ntseq <- c("AAAATTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGTGTGCGCTGC")
out <- Tm_NN(ntseq,Na=50)
out
out$Options

Calculate the melting temperature using the 'Wallace rule'

Description

The Wallace rule is often used as rule of thumb for approximate melting temperature calculations for primers with 14 to 20 nt length.

Usage

Tm_Wallace(ntseq, ambiguous = FALSE, outlist = TRUE)

Arguments

ntseq

Sequence (5' to 3') of one strand of the DNA nucleic acid duplex as string or vector of characters (Note: Non-DNA characters are ignored by this method).

ambiguous

Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.

outlist

output a list of Tm and options or only Tm value, default is TRUE.

Author(s)

Junhui Li

References

Thein S L , Lynch J R , Weatherall D J , et al. DIRECT DETECTION OF HAEMOGLOBIN E WITH SYNTHETIC OLIGONUCLEOTIDES[J]. The Lancet, 1986, 327(8472):93.

Examples


ntseq = c('acgtTGCAATGCCGTAWSDBSY') #for wallace rule

out <- Tm_Wallace(ntseq,ambiguous = TRUE)
out
out$Options

convert a vector of characters into a string

Description

Simply convert a vector of characters such as c("H","e","l","l","o","W","o","r","l","d") into a single string "HelloWorld".

Usage

c2s(characters)

Arguments

characters

A vector of characters

Value

Retrun a strings

Author(s)

Junhui Li

References

citation("TmCalculator")

Examples


c2s(c("H","e","l","l","o","W","o","r","l","d"))

Check and filter invalid base of nucleotide sequences

Description

In general, whitespaces and non-base characters are removed and characters are converted to uppercase in given method.

Usage

check_filter(ntseq, method)

Arguments

ntseq

Sequence (5' to 3') of one strand of the DNA nucleic acid duplex as string or vector of characters

method

TM_Wallace: check and return "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W" and "Y"

TM_GC: check and return "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W", "X" and "Y"

TM_NN: check and return "A","C","G","I" and "T"

Value

Return a sequence which fullfils the requirements of the given method.

Author(s)

Junhui Li

References

citation("TmCalculator")

Examples


ntseq <- c("ATCGBDHKMNRVYWSqq")
check_filter(ntseq,method='Tm_Wallace')
check_filter(ntseq,method='Tm_NN')

Corrections of melting temperature with chemical substances

Description

Corrections coefficient of melting temperature with DMSO and formamide and these corrections are rough approximations.

Usage

chem_correction(
  DMSO = 0,
  fmd = 0,
  DMSOfactor = 0.75,
  fmdmethod = c("concentration", "molar"),
  fmdfactor = 0.65,
  ptGC
)

Arguments

DMSO

Percent DMSO

fmd

Formamide concentration in percentage (fmdmethod="concentration") or molar (fmdmethod="molar").

DMSOfactor

Coefficient of Tm decreases per percent DMSO. Default=0.75 von Ahsen N (2001) <PMID:11673362>. Other published values are 0.5, 0.6 and 0.675.

fmdmethod

"concentration" method for formamide concentration in percentage and "molar" for formamide concentration in molar

fmdfactor

Coefficient of Tm decrease per percent formamide. Default=0.65. Several papers report factors between 0.6 and 0.72.

ptGC

Percentage of GC(%).

Details

fmdmethod = "concentration"

Correction = - factor*percentage_of_formamide

fmdmethod = "molar"

Correction = (0.453*GC/100 - 2.88) x formamide

Author(s)

Junhui Li

References

Examples

chem_correction(DMSO=3)
chem_correction(fmd=1.25, fmdmethod="molar", ptGC=50)

complement and reverse complement base of nucleotide sequences

Description

get reverse complement and complement base of nucleotide sequences

Usage

complement(ntseq, reverse = FALSE)

Arguments

ntseq

Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters

reverse

Logical value, TRUE is reverse complement sequence, FALSE is not.

Author(s)

Junhui Li

References

citation("TmCalculator")

Examples


complement("ATCGYCGYsWwsaVv")
complement("ATCGYCGYsWwsaVv",reverse=TRUE)

Prints melting temperature from a `TmCalculator` object

Description

print.TmCalculator prints to console the melting temperature value from an object of class TmCalculator.

Usage

## S3 method for class 'TmCalculator'
print(x, ...)

Arguments

x

An object of class TmCalculator.

...

Unused

Value

The melting temperature value.

convert a string into a vector of characters

Description

Simply convert a single string such as "HelloWorld" into a vector of characters such as c("H","e","l","l","o","W","o","r","l","d")

Usage

s2c(strings)

Arguments

strings

A single string such as "HelloWorld"

Value

Retrun a vector of characters

Author(s)

Junhui Li

References

citation("TmCalculator")

Examples


s2c(c("HelloWorld"))

Corrections of melting temperature with salt ions

Description

Corrections coefficient of melting temperature or entropy with different operations

Usage

salt_correction(
  Na = 0,
  K = 0,
  Tris = 0,
  Mg = 0,
  dNTPs = 0,
  method = c("Schildkraut2010", "Wetmur1991", "SantaLucia1996", "SantaLucia1998-1",
    "SantaLucia1998-2", "Owczarzy2004", "Owczarzy2008"),
  ntseq,
  ambiguous = FALSE
)

Arguments

Na

Millimolar concentration of Na

K

Millimolar concentration of K

Tris

Millimolar concentration of Tris

Mg

Millimolar concentration of Mg

dNTPs

Millimolar concentration of dNTPs

method

Method to be applied including "Schildkraut2010", "Wetmur1991","SantaLucia1996", "SantaLucia1998-1", "SantaLucia1998-2","Owczarzy2004","Owczarzy2008". First fourth methods correct Tm, fifth method corrects deltaS, sixth and seventh methods correct 1/Tm. See details for the method description.

ntseq

Sequence (5' to 3') of one strand of the nucleic acid duplex as string or vector of characters.

ambiguous

Ambiguous bases are taken into account to compute the G and C content when ambiguous is TRUE.

Details

The methods are:

1 Schildkraut C (2010) <doi:10.1002/bip.360030207>

2 Wetmur J G (1991) <doi:10.3109/10409239109114069>

3 SantaLucia J (1996) <doi:10.1021/bi951907q>

4 SantaLucia J (1998) <doi:10.1073/pnas.95.4.1460>

5 SantaLucia J (1998) <doi:10.1073/pnas.95.4.1460>

6 Owczarzy R (2004) <doi:10.1021/bi034621r>

7 Owczarzy R (2008) <doi:10.1021/bi702363u>

methods 1-4: Tm(new) = Tm(old) + correction

method 5: deltaS(new) = deltaS(old) + correction

methods 6+7: Tm(new) = 1/(1/Tm(old) + correction)

Author(s)

Junhui Li

References

Schildkraut C . Dependence of the melting temperature of DNA on salt concentration[J]. Biopolymers, 2010, 3(2):195-208.

Wetmur J G . DNA Probes: Applications of the Principles of Nucleic Acid Hybridization[J]. CRC Critical Reviews in Biochemistry, 1991, 26(3-4):3

Santalucia , J , Allawi H T , Seneviratne P A . Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, [J]. Biochemistry, 1996, 35(11):3555-3562.

SantaLucia, J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics[J]. Proceedings of the National Academy of Sciences, 1998, 95(4):1460-1465.

Owczarzy R , You Y , Moreira B G , et al. Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions ofMelting Temperatures[J]. Biochemistry, 2004, 43(12):3537-3554.

Owczarzy R , Moreira B G , You Y , et al. Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations[J]. Biochemistry, 2008, 47(19):5336-5353.

Examples


ntseq <- c("acgtTGCAATGCCGTAWSDBSYXX")
salt_correction(Na=390, K=20, Tris=0, Mg=10, dNTPs=25, method="Owczarzy2008", ntseq)

Calculate G and C content of nucleotide sequences

Description

Usage

Arguments

Value

Author(s)

Examples

Calculate the melting temperature using empirical formulas based on GC content

Description

Usage

Arguments

Details

Author(s)

References

Examples

Calculate melting temperature using nearest neighbor thermodynamics

Description

Usage

Arguments

Details

Author(s)

References

Examples

Calculate the melting temperature using the 'Wallace rule'

Description

Usage

Arguments

Author(s)

References

Examples

convert a vector of characters into a string

Description

Usage

Arguments

Value

Author(s)

References

Examples

Check and filter invalid base of nucleotide sequences

Description

Usage

Arguments

Value

Author(s)

References

Examples

Corrections of melting temperature with chemical substances

Description

Usage

Arguments

Details

Author(s)

References

Examples

complement and reverse complement base of nucleotide sequences

Description

Usage

Arguments

Author(s)

References

Examples

Prints melting temperature from a TmCalculator object

Description

Usage

Arguments

Value

convert a string into a vector of characters

Description

Usage

Arguments

Value

Author(s)

References

Examples

Corrections of melting temperature with salt ions

Description

Usage

Arguments

Details

Author(s)

Prints melting temperature from a `TmCalculator` object