TmCalculator v1.0.0

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Melting Temperature of Nucleic Acid Sequences

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) <10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <PMID:11673362>) 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>).

Functions in TmCalculator

Name Description
Tm_GC Calculate the melting temperature using empirical formulas based on GC content
Tm_NN Calculate melting temperature using nearest neighbor thermodynamics
check_filter Check and filter valid base of nucleotide sequences
chem_correction Correct melting temperature with chemical substances
complement reverse complement and complement base of nucleotide sequences
s2c convert a string into a vector of characters
GC Calculate G and C content of nucleotide sequences
TmCalculator-package Melting Temperature of Nucleic Acid Sequences
salt_correction Calculate the corrected melting temperature with salt ions
Tm_Wallace Calculate the melting temperature using the 'Wallace rule'
c2s convert a vector of characters into a string
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Details

Type Package
Date 2019-01-25
License GPL (>= 2)
NeedsCompilation no
Packaged 2019-02-05 05:10:32 UTC; lenovo
Repository CRAN
Date/Publication 2019-02-11 13:53:18 UTC
depends R (>= 2.10)
Contributors Junhui Li

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