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TmCalculator (version 1.0.0)

Melting Temperature of Nucleic Acid Sequences

Description

The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) ), empirical formulas based on G and C content (Marmur J. (1962) , Schildkraut C. (2010) , Wetmur J G (1991) <10.3109/10409239109114069>, Untergasser,A. (2012) , von Ahsen N (2001) ) and nearest neighbor thermodynamics (Breslauer K J (1986) , Sugimoto N (1996) , Allawi H (1998) , SantaLucia J (2004) , Freier S (1986) , Xia T (1998) , Chen JL (2012) , Bommarito S (2000) , Turner D H (2010) , Sugimoto N (1995) , Allawi H T (1997) , Santalucia N (2005) ), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) , SantaLucia J(1998) , Owczarzy R (2004) , Owczarzy R (2008) ).

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Version

Install

install.packages('TmCalculator')

Monthly Downloads

265

Version

1.0.0

License

GPL (>= 2)

Maintainer

JunhuiLi

Last Published

February 11th, 2019

Functions in TmCalculator (1.0.0)

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