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TmCalculator  

Melting Temperature of Nucleic Acid Sequences
View on CRAN: Click here


Download and install TmCalculator package within the R console
Install from CRAN:
install.packages("TmCalculator")

Install from Github:
library("remotes")
install_github("cran/TmCalculator")

Install by package version:
library("remotes")
install_version("TmCalculator", "1.0.3")



Attach the package and use:
library("TmCalculator")
Maintained by
Junhui Li
[Scholar Profile | Author Map]
First Published: 2019-02-11
Latest Update: 2022-02-21
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>).
How to cite:
Junhui Li (2019). TmCalculator: Melting Temperature of Nucleic Acid Sequences. R package version 1.0.3, https://cran.r-project.org/web/packages/TmCalculator. Accessed 07 Apr. 2025.
Previous versions and publish date:
1.0.0 (2019-02-11 14:53), 1.0.1 (2020-07-31 06:40), 1.0.2 (2022-01-21 00:02)
Other packages that cited TmCalculator R package
View TmCalculator citation profile
Other R packages that TmCalculator depends, imports, suggests or enhances
Complete documentation for TmCalculator
Functions, R codes and Examples using the TmCalculator R package
Some associated functions: GC . Tm_GC . Tm_NN . Tm_Wallace . c2s . check_filter . chem_correction . complement . print.TmCalculator . s2c . salt_correction . 
Some associated R codes: GC.R . Tm_GC.R . Tm_NN.R . Tm_Wallace.R . c2s.R . check_filter.R . chem_correction.R . complement.R . print.TmCalculator.R . s2c.R . salt_correction.R .  Full TmCalculator package functions and examples
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