melting.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/melting.R
\encoding{UTF-8}
\name{melting}
\alias{melting}
\title{melting}
\usage{
melting(sequence, comp.sequence = NULL,
         nucleic.acid.conc,
         hybridisation.type = c("dnadna", "rnarna", "dnarna",
                               "rnadna", "mrnarna", "rnamrna"),
         Na.conc, Mg.conc, Tris.conc, K.conc,
         dNTP.conc, DMSO.conc, formamide.conc,
         size.threshold = 60, self = FALSE, correction.factor,
         method.approx = c("ahs01", "che93", "che93corr",
                           "marschdot", "owe69", "san98",
                           "wetdna91", "wetrna91", "wetdnarna91"),
         method.nn = c("all97", "bre86", "san04", "san96", "sug96",
                      "tan04", "fre86", "xia98", "sug95", "tur06"),
         method.GU = c("tur99"),
         method.singleMM = c("allsanpey", "tur06", "zno07", "zno08"),
         method.tandemMM = c("allsanpey", "tur99"),
         method.single.dangle = c("bom00", "sugdna02", "sugrna02", "ser08"),
         method.double.dangle = c("sugdna02", "sugrna02", "ser05", "ser06"),
         method.long.dangle = c("sugdna02", "sugrna02"),
         method.internal.loop = c("san04", "tur06", "zno07"),
         method.single.bulge.loop = c("tan04", "san04", "ser07" ,"tur06"),
         method.long.bulge.loop = c("san04", "tur06"),
         method.CNG = c("bro05"),
         method.inosine = c("san05", "zno07"),
         method.hydroxyadenine = c("sug01"),
         method.azobenzenes = c("asa05"),
         method.locked = c("mct04"),
         correction.Na = c("ahs01", "kam71", "marschdot",
                           "owc1904", "owc2004", "owc2104", "owc2204",
                           "san96", "san04", "schlif",
                           "tanna06", "tanna07", "wet91"),
         correction.Mg = c("oxcmg08", "tanmg06", "tanmg07"),
         correction.NaMg = c("oxcmix08", "tanmix07"),
         method.Naeq = c("ahs01", "mit96", "pey00"),
         correction.DMSO = c("ahs01", "cul76", "esc80", "mus80"),
}
\arguments{
\item{sequence}{Sequence (5' to 3') of one strand of the nucleic acid duplex
as a character string.}

\item{comp.sequence}{Complementary sequence (3' to 5') of the nucleic acid
duplex as a character string.}

\item{nucleic.acid.conc}{Concentration of the nucleic acid strand
(\ifelse{html}{mol L<sup>-1</sup>}{\eqn{\textrm{mol L}^{-1}}}) in excess as
a numeric value.}

\item{hybridisation.type}{The hybridisation type. Either \code{"dnadna"},
\code{"rnarna"},  \code{"dnarna"}, \code{"rnadna"}, \code{"mrnarna"} or
\code{"rnamrna"} (see \strong{Hybridisation type options}).}

\item{Na.conc}{Concentration of Na ions (M) as a numeric value (see
\strong{Ion and agent concentrations}).}

\item{Mg.conc}{Concentration of Mg ions (M) as a numeric value (see
\strong{Ion and agent concentrations}).}

\item{Tris.conc}{Concentration of Tris ions (M) as a numeric value  (see
\strong{Ion and agent concentrations}).}

\item{K.conc}{Concentration of K ions (M) as a numeric value (see \strong{Ion
and agent concentrations}).}

\item{dNTP.conc}{Concentration of dNTP (M) as a numeric value (see \strong{Ion
and agent concentrations}).}

\item{DMSO.conc}{Concentration of DMSO (\%) as a numeric value (see
\strong{Ion and agent concentrations}).}

\item{formamide.conc}{Concentration of formamide (M or \% depending on
correction method) as a numeric value (see \strong{Ion and agent
concentrations}).}

\item{size.threshold}{Sequence length threshold to decide approximative or
nearest-neighbour approach for computation. Default is 60.}

\item{self}{logical. Specifies that \code{sequence} is self complementary and
\code{complementary sequence} is not required (seed \strong{Self
complementary sequences}). Default is \code{FALSE}.}

\item{correction.factor}{Correction factor to be used to modulate the effect
of the nucleic acid concentration (\code{nucleic.acid.conc}) in the
computation of melting temperature (see \strong{Correction factor for
nucleic acid concentration}).}

\item{method.approx}{Specify the approximative formula to be used for melting
temperature calculation for sequences of length greater than
\code{size.threshold}. Either \code{"ahs01"}, \code{"che93"},
\code{"che93corr"}, \code{"schdot"}, \code{"owe69"}, \code{"san98"},
\code{"wetdna91"}, \code{"wetrna91"} or \code{"wetdnarna91"} (see
\strong{Approximative formulas}).}

\item{method.nn}{Specify the nearest neighbor model to be used for melting
temperature calculation for sequences of length lesser than
\code{size.threshold}. Either \code{"all97"}, \code{"bre86"},
\code{"san04"}, \code{"san96"}, \code{"sug96"}, \code{"tan04"},
\code{"fre86"}, \code{"xia98"}, \code{"sug95"} or \code{"tur06"} (see
\strong{Nearest neighbor models}).}

\item{method.GU}{Specify the nearest neighbor model to compute the
contribution of GU base pairs to the thermodynamic of helix-coil transition.
Available method is \code{"tur99"} (see \strong{GU wobble base pairs
effect}).}

\item{method.singleMM}{Specify the nearest neighbor model to compute the
contribution of single mismatch to the thermodynamic of helix-coil
transition.  Either \code{"allsanpey"}, \code{"tur06"}, \code{"zno07"} or
\code{"zno08"} (see \strong{Single mismatch effect}).}

\item{method.tandemMM}{Specify the nearest neighbor model to compute the
contribution of tandem mismatches to the thermodynamic of helix-coil
transition. Either \code{"allsanpey"} or \code{"tur99"} (see \strong{Tandem
mismatches effect}).}

\item{method.single.dangle}{Specify the nearest neighbor model to compute the
contribution of single dangling end to the thermodynamic of helix-coil
transition. Either \code{"bom00"}, \code{"sugdna02"}, \code{"sugrna02"} or
\code{"ser08"} (see \strong{Single dangling end effect}).}

\item{method.double.dangle}{Specify the nearest neighbor model to compute the
contribution of double dangling end to the thermodynamic of helix-coil
transition. Either \code{"sugdna02"}, \code{"sugrna02"}, \code{"ser05"} or
\code{"ser06"} (see \strong{Double dangling end effect}).}

\item{method.long.dangle}{Specify the nearest neighbor model to compute the
contribution of long dangling end to the thermodynamic of helix-coil
transition. Either \code{"sugdna02"} or \code{"sugrna02"} (see \strong{Long
dangling end effect}).}

\item{method.internal.loop}{Specify the nearest neighbor model to compute the
contribution of internal loop to the thermodynamic of helix-coil transition.
Either \code{"san04"}, \code{"tur06"} or \code{"zno07"} (see
\strong{Internal loop effect}).}

\item{method.single.bulge.loop}{Specify the nearest neighbor model to compute
the contribution of single bulge loop to the thermodynamic of helix-coil
transition. Either \code{"san04"}, \code{"tan04"}, \code{"ser07"} or
\code{"tur06"} (see \strong{Single bulge loop effect}).}

\item{method.long.bulge.loop}{Specify the nearest neighbor model to compute
the contribution of long bulge loop to the thermodynamic of helix-coil
transition. Either \code{"san04"} or \code{"tur06"} (see \strong{Long bulge
loop effect}).}

\item{method.CNG}{Specify the nearest neighbor model to compute the
contribution of CNG repeats to the thermodynamic of helix-coil transition.
Available method is \code{"bro05"} (see \strong{CNG repeats effect}).}

\item{method.inosine}{Specify the pecific nearest neighbor model to compute
the contribution of inosine bases (I) to the thermodynamic of helix-coil
transition. Either \code{"san05"} or \code{"zno07"} (see \strong{Inosine
bases effect}).}

\item{method.hydroxyadenine}{Specify the nearest neighbor model to compute the
contribution of hydroxyadenine bases (A*) to the thermodynamic of helix-coil
transition. Available method is \code{"sug01"} (see \strong{Hydroxyadenine
bases effect}).}

\item{method.azobenzenes}{Specify the nearest neighbor model to compute the
contribution of azobenzenes (X_T for trans azobenzenes and X_C for cis
azobenzenes) to the thermodynamic of helix-coil transition. Available method
is \code{"asa05"} (see \strong{Azobenzenes effect}).}

\item{method.locked}{Specify the nearest neighbor model to compute the
contribution of locked nucleic acids (AL, GL, TL and CL) to the
thermodynamic of helix-coil transition. Available method is \code{"mct04"}
(see \strong{Locked nucleic acids effect}).}

\item{correction.Na}{Specify the correction method for Na ions. Either
\code{"ahs01"}, \code{"kam71"}, \code{"owc1904"}, \code{"owc2004"},
\code{"owc2104"}, \code{"owc2204"}, \code{"san96"}, \code{"san04"},
\code{"schlif"}, \code{"tanna06"}, \code{"wetdna91"}, \code{"tanna07"},
\code{"wetrna91"} or \code{"wetdnarna91"} (see \strong{Sodium corrections}).}

\item{correction.Mg}{Specify the correction method for Mg ions. Either
\code{"owcmg08"}, \code{"tanmg06"} or \code{"tanmg07"} (see
\strong{Magnesium corrections}).}

\item{correction.NaMg}{Specify the correction method for mixed Na and Mg ions.
Either \code{"owcmix08"}, \code{"tanmix07"} or \code{"tanmix07"} (see
\strong{Mixed Sodium and Magnesium corrections}).}

\item{method.Naeq}{Specify the ion correction which gives a sodium equivalent
concentration if other cations are present. Either \code{"ahs01"},
\code{"mit96"} or \code{"pey00"} (see \strong{Sodium equivalent
concentration methods}).}

\item{correction.DMSO}{Specify the correction method for DMSO. Specify the
correction method for DMSO. Either \code{"ahs01"}, \code{"mus81"},
\code{"cul76"} or \code{"esc80"} (see \strong{DMSO corrections}).}

\item{correction.formamide}{Specify the correction method for formamide.
Specify the correction method for formamide Either \code{"bla96"} or
\code{"lincorr"} (see \strong{Formamide corrections}).}
}
\description{
R interface to the
\href{https://www.ebi.ac.uk/biomodels/tools/melting/}{MELTING 5 software} (Le
Novère, 2001; Dumousseau et al., 2012) for computation of enthalpy and entropy
of the helix-coil transition, and then the melting temperature of a nucleic
acid duplex.
}
\section{Mandatory arguments}{
 The following are the arguments which are
 mandatory for computation. \itemize{ \item \code{sequence} \item
 \code{comp.sequence}: Mandatory if there are mismatches, inosine(s) or
 hydroxyadenine(s) between the two strands. If not specified, it is computed
 as the complement of \code{sequence}. Self-complementarity in
 \code{sequence} is detected even though there may be (are) dangling end(s)
 and \code{comp.sequence} is computed (see \strong{Self complementary
 sequences}). \item \code{nucleic.acid.conc} \item \code{Na.conc, Mg.conc,
 Tris.conc, K.conc}: At least one cation (Na, Mg, Tris, K) concentration is
 mandatory, the other agents(dNTP, DMSO, formamide) are optional. \item
 \code{hybridisation.type} }
}

\section{Hybridisation type options}{
 The details of the possible options for
 hybridisation type specified in the argument \code{hybridisation.type} are
 as follows:

 \tabular{lll}{ \strong{Option} \tab \strong{\code{Sequence}} \tab
 \strong{\code{Complementary sequence}}\cr \code{dnadna} \tab DNA \tab DNA
 \cr \code{rnarna} \tab RNA \tab RNA \cr \code{dnarna} \tab DNA \tab RNA \cr
 \code{rnadna} \tab RNA \tab DNA \cr \code{mrnarna} \tab 2-o-methyl RNA \tab
 RNA \cr \code{rnamrna} \tab RNA \tab 2-o-methyl RNA }

 This parameter determines the nature of the sequences in the arguments
 \code{sequence} and \code{comp.sequence}.
}

\section{Ion and agent concentrations}{
 These values are used for different
 correction functions which approximately adjusts for effects of these
 ions(Na, Mg, Tris, K) and/or agents(dNTP, DMSO, formamide) on on
 thermodynamic stability of nucleic acid duplexes. Their concentration limits
 depends on the correction method used. All the concentrations must be in M,
 except for the DMSO (\%) and formamide (\% or M depending on the correction
 method). Note that Tris+ concentration is about half of the total tris
 buffer concentration.
}

\section{Self complementary sequences}{
 Self complementarity for perfect
 matching sequences or sequences with dangling ends is detected
 automatically. However it can be specified by the argument \code{self}.
}

\section{Correction factor for nucleic acid concentration}{
 For self
 complementary sequences (Auto detected or specified in \code{self}) it is 1.
 Otherwise it is 4 if the both strands are present in equivalent amount and 1
 if one strand is in excess.
}

\section{Approximative estimation formulas}{
 The calculation is increasingly
 incorrect when the length of the duplex decreases. Moreover, it does not
 take into account nucleic acid concentration. \tabular{llll}{
 \strong{Formula}\tab \strong{Type} \tab \strong{Limits.Remarks}\tab
 \strong{Reference}\cr \code{ahs01}\tab DNA\tab No mismatch \tab von Ahsen et
 al., 2001 \cr \code{che93}\tab DNA\tab No mismatch; Na=0, Mg=0.0015, \tab
 Marmur and Doty, 1962\cr \tab\tab Tris=0.01, K=0.05 \tab\cr
 \code{che93corr}\tab DNA\tab No mismatch; Na=0, Mg=0.0015, \tab Marmur and
 Doty, 1962\cr \tab\tab Tris=0.01, K=0.05 \tab\cr \code{marschdot}\tab
 DNA\tab No mismatch \tab Wetmur, 1991; Marmur and \cr \tab\tab \tab Doty,
 1962; Chester and\cr \tab\tab \tab Marshak, 1993; Schildkraut \cr \tab\tab
 \tab and Lifson, 1965; Wahl et\cr \tab\tab \tab al., 1987; Britten et al.,
 \cr \tab\tab \tab 1974; Hall et al., 1980\cr \code{owe69}\tab DNA\tab No
 mismatch \tab Owen et al., 1969; \cr \tab\tab \tab Frank-Kamenetskii, 1971;
 \cr \tab\tab \tab Blake, 1996; Blake and \cr \tab\tab \tab Delcourt, 1998
 \cr \code{san98}\tab DNA\tab No mismatch \tab SantaLucia, 1998; von Ahsen\cr
 \tab\tab \tab et al., 2001 \cr \code{wetdna91}*\tab DNA\tab \tab Wetmur,
 1991 \cr \code{wetrna91}*\tab RNA\tab \tab Wetmur, 1991 \cr
 \code{wetdnarna91}* \tab DNA/RNA\tab \tab Wetmur, 1991 }
}

\section{Nearest neighbor models}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference}\cr
 \code{all97}*\tab DNA\tab\tab Allawi and SantaLucia, 1997\cr
 \code{tur06}*\tab 2'-O-MeRNA/\tab A sodium correction\tab Kierzek et al.,
 2006 \cr \tab RNA\tab (\code{san04}) is \tab\cr \tab\tab automatically
 applied to \tab\cr \tab\tab convert the entropy (Na =\tab\cr \tab\tab 0.1M)
 into the entropy (Na = \tab\cr \tab\tab 1M). \tab\cr \code{bre86} \tab
 DNA\tab\tab Breslauer et al., 1986 \cr \code{san04} \tab DNA\tab\tab
 SantaLucia and Hicks, 2004 \cr \code{san96} \tab DNA\tab\tab SantaLucia et
 al., 1996\cr \code{sug96} \tab DNA\tab\tab Sugimoto et al., 1996\cr
 \code{tan04} \tab DNA\tab\tab Tanaka et al., 2004\cr \code{fre86} \tab
 RNA\tab\tab Freier et al., 1986\cr \code{xia98}*\tab RNA\tab\tab Xia et al.,
 1998 \cr \code{sug95}*\tab DNA/ \tab\tab SantaLucia et al., 1996\cr \tab
 RNA\tab\tab }
}

\section{GU wobble base pairs effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{tur99}*\tab RNA\tab\tab Mathews et al., 1999 }
}

\section{Single mismatch effect}{
 \tabular{llll}{ \strong{Model}\tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference} \cr
 \code{allsanpey}* \tab DNA\tab \tab Allawi and SantaLucia, 1997;\cr \tab\tab
 \tab Allawi and SantaLucia, 1998;\cr \tab\tab \tab Allawi and SantaLucia,
 1998;\cr \tab\tab \tab Allawi and SantaLucia, \cr \tab\tab \tab 1998; Peyret
 et al., 1999 \cr \code{tur06}\tab RNA\tab \tab Lu et al., 2006 \cr
 \code{zno07}* \tab RNA\tab \tab Davis and Znosko, 2007\cr \code{zno08}\tab
 RNA\tab At least one adjacent GU base \tab Davis and Znosko, 2008\cr
 \tab\tab pair. \tab }
}

\section{Tandem mismatches effect}{
 \tabular{llll}{ \strong{Model}\tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{allsanpey}* \tab DNA\tab Only GT mismatches and TA/TG \tab Allawi and
 SantaLucia, 1997;\cr \tab\tab mismatches.\tab Allawi and SantaLucia,
 1998;\cr \tab\tab\tab Allawi and SantaLucia, 1998;\cr \tab\tab\tab Allawi
 and SantaLucia, \cr \tab\tab\tab 1998; Peyret et al., 1999 \cr \code{tur99}*
 \tab RNA\tab No adjacent GU or UG base\tab Mathews et al., 1999\cr \tab\tab
 pairs. \tab } Tandem mismatches are not taken into account by the
 approximative mode. Note that not all the mismatched Crick's pairs have been
 investigated.
}

\section{Single dangling end effect}{
 \tabular{llll}{ \strong{Model}\tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference} \cr
 \code{bom00}* \tab DNA\tab \tab Bommarito et al., 2000\cr \code{sugdna02}
 \tab DNA\tab Only terminal poly A self \tab Ohmichi et al., 2002\cr \tab\tab
 complementary sequences.\tab \cr \code{sugrna02} \tab RNA\tab Only terminal
 poly A self \tab Ohmichi et al., 2002\cr \tab\tab complementary
 sequences.\tab \cr \code{ser08}* \tab RNA\tab Only 3' UA, GU and UG \tab
 Miller et al., 2008 \cr \tab\tab terminal base pairs only 5' \tab \cr
 \tab\tab UG and GU terminal base \tab \cr \tab\tab pairs.\tab } Single
 dangling ends are not taken into account by the approximative mode.
}

\section{Double dangling end effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{sugdna02}* \tab DNA\tab Only terminal poly A self\tab Ohmichi et al.,
 2002\cr \tab\tab complementary sequences. \tab \cr \code{sugrna02}\tab
 RNA\tab Only terminal poly A self\tab Ohmichi et al., 2002\cr \tab\tab
 complementary sequences. \tab \cr \code{ser05} \tab RNA\tab Depends on the
 available \tab O'Toole et al., 2005\cr \tab\tab thermodynamic parameters for
 \tab \cr \tab\tab single dangling end. \tab \cr \code{ser06}*\tab
 RNA\tab\tab O'Toole et al., 2006 } Double dangling ends are not taken into
 account by the approximative mode.
}

\section{Long dangling end effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference} \cr
 \code{sugdna02}* \tab DNA\tab Only terminal poly A self \tab Ohmichi et al.,
 2002\cr \tab\tab complementary sequences.\tab \cr \code{sugrna02}* \tab
 RNA\tab Only terminal poly A self \tab Ohmichi et al., 2002\cr \tab\tab
 complementary sequences.\tab } Long dangling ends are not taken into account
 by the approximative mode.
}

\section{Internal loop effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{san04}*\tab DNA\tab Missing asymmetry penalty. \tab SantaLucia and
 Hicks, 2004\cr \tab\tab Not tested with experimental \tab \cr \tab\tab
 results. \tab \cr \code{tur06} \tab RNA\tab Not tested with experimental
 \tab Lu et al., 2006 \cr \tab\tab results. \tab \cr \code{zno07}*\tab
 RNA\tab\tab Davis and Znosko, 2007 } Internal loops are not taken into
 account by the approximative mode.
}

\section{Single bulge loop effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference} \cr
 \code{tan04}*\tab DNA\tab \tab Tan and Chen, 2007\cr \code{san04} \tab
 DNA\tab Missing closing AT penalty. \tab SantaLucia and Hicks, 2004\cr
 \code{ser07} \tab RNA\tab Less reliable results. Some \tab Blose et al.,
 2007\cr \tab\tab missing parameters. \tab \cr \code{tur06}*\tab RNA\tab \tab
 Lu et al., 2006 } Internal loops are not taken into account by the
 approximative mode.
}

\section{Long bulge loop effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{san04}*\tab DNA\tab Missing closing AT penalty.\tab SantaLucia and
 Hicks, 2004\cr \code{tur06}*\tab RNA\tab Not tested with experimental \tab
 Lu et al., 2006 \cr \tab\tab results. \tab } Long bulge loops are not taken
 into account by the approximative mode.
}

\section{CNG repeats effect}{
 \tabular{llll}{ \strong{Model} \tab \strong{Type}
 \tab \strong{Limits.Remarks}\tab \strong{Reference}\cr \code{bro05}*\tab
 RNA\tab Self complementary sequences. \tab Broda et al., 2005 \cr \tab\tab 2
 to 7 CNG repeats. \tab } CNG repeats are not taken into account by the
 approximative mode. The contribution of CNG repeats to the thermodynamic of
 helix-coil transition can be computed only for 2 to 7 CNG repeats. N
 represents a single mismatch of type N/N.
}

\section{Inosine bases effect}{
  \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference} \cr
 \code{san05}*\tab DNA\tab Missing parameters for tandem \tab Watkins and
 SantaLucia, 2005\cr \tab\tab base pairs containing inosine \tab \cr \tab\tab
 bases.\tab \cr \code{zno07}*\tab RNA\tab Only IU base pairs. \tab Wright et
 al., 2007 }
}

\section{Hydroxyadenine bases effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference}\cr
 \code{sug01}*\tab DNA\tab Only 5' GA*C 3'and 5' TA*A 3' \tab Kawakami et
 al., 2001\cr \tab\tab contexts. \tab } Hydroxyadenine bases (A*) are not
 taken into account by the approximative mode.
}

\section{Azobenzenes effect effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{asa05}*\tab DNA\tab Less reliable results when \tab Asanuma et al.,
 2005\cr \tab\tab the number of cis azobenzene \tab \cr \tab\tab increases.
 \tab } Azobenzenes (X_T for trans azobenzenes and X_C for cis azobenzenes)
 are not taken into account by the approximative mode.
}

\section{Locked nucleic acids effect}{
 \tabular{llll}{ \strong{Model} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{mct04}*\tab DNA\tab\tab McTigue et al., 2004 } Locked nucleic acids
 (AL, GL, TL and CL) are not taken into account by the approximative mode.
}

\section{Sodium corrections}{
 \tabular{llll}{ \strong{Correcion} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference} \cr
 \code{ahs01} \tab DNA\tab Na>0.\tab von Ahsen et al., 2001\cr
 \code{schlif}\tab DNA\tab Na>=0.07; Na<=0.12.\tab Schildkraut and Lifson,
 1965\cr \code{tanna06} \tab DNA\tab Na>=0.001; Na<=1.\tab Tan and Chen,
 2006\cr \code{tanna07}*\tab RNA\tab Na>=0.003; Na<=1.\tab Tan and Chen,
 2007\cr \tab or \tab\tab \cr \tab 2'-O-MeRNA/RNA \tab\tab \cr \code{wet91}
 \tab RNA, \tab Na>0.\tab Wetmur, 1991\cr \tab DNA\tab\tab \cr \tab
 and\tab\tab \cr \tab RNA/DNA\tab\tab \cr \code{kam71} \tab DNA\tab Na>0;
 Na>=0.069; Na<=1.02. \tab Frank-Kamenetskii, 1971 \cr \code{marschdot} \tab
 DNA\tab Na>=0.069; Na<=1.02. \tab Marmur and Doty, 1962; Blake\cr
 \tab\tab\tab and Delcourt, 1998\cr \code{owc1904} \tab DNA\tab Na>0.\tab
 Owczarzy et al., 2004 \cr \code{owc2004} \tab DNA\tab Na>0.\tab Owczarzy et
 al., 2004 \cr \code{owc2104} \tab DNA\tab Na>0.\tab Owczarzy et al., 2004
 \cr \code{owc2204}*\tab DNA\tab Na>0.\tab Owczarzy et al., 2004 \cr
 \code{san96} \tab DNA\tab Na>=0.1. \tab SantaLucia et al., 1996 \cr
 \code{san04} \tab DNA\tab Na>=0.05; Na<=1.1; \tab SantaLucia and Hicks,
 2004; \cr \tab\tab Oligonucleotides inferior to \tab SantaLucia, 1998\cr
 \tab\tab 16 bases.\tab }
}

\section{Magnesium corrections}{
 \tabular{llll}{ \strong{Correcion} \tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference}\cr
 \code{owcmg08}*\tab DNA\tab Mg>=0.0005; Mg<=0.6.\tab Owczarzy et al.,
 2008\cr \code{tanmg06} \tab DNA\tab Mg>=0.0001; Mg<=1; Oligomer \tab Tan and
 Chen, 2006 \cr \tab\tab length superior to 6 base \tab\cr \tab\tab
 pairs.\tab\cr \code{tanmg07}*\tab RNA\tab Mg>=0.1; Mg<=0.3. \tab Tan and
 Chen, 2007 }
}

\section{Mixed Sodium and Magnesium corrections}{
 \tabular{llll}{
 \strong{Correcion} \tab \strong{Type} \tab \strong{Limits.Remarks} \tab
 \strong{Reference}\cr \code{owcmix08}* \tab DNA\tab Mg>=0.0005; Mg<=0.6;
 \tab Owczarzy et al., 2008\cr \tab\tab Na+K+Tris/2>0. \tab\cr
 \code{tanmix07}\tab DNA\tab Mg>=0.1; Mg<=0.3;\tab Tan and Chen, 2007 \cr
 \tab and\tab Na+K+Tris/2>=0.1;\tab\cr \tab RNA\tab Na+K+Tris/2<=0.3.\tab }
}

\section{Sodium equivalent concentration methods}{
 \tabular{llll}{
 \strong{Correcion} \tab \strong{Type} \tab \strong{Limits.Remarks} \tab
 \strong{Reference} \cr \code{ahs01}*\tab DNA\tab\tab von Ahsen et al.,
 2001\cr \code{mit96} \tab DNA\tab\tab Mitsuhashi, 1996\cr \code{pey00} \tab
 DNA\tab\tab Peyret, 2000 }
}

\section{DMSO corrections}{
 \tabular{llll}{ \strong{Correcion} \tab
 \strong{Type} \tab \strong{Limits.Remarks} \tab \strong{Reference}\cr
 \code{ahs01} \tab DNA\tab Not tested with experimental \tab von Ahsen et
 al., 2001 \cr \tab\tab results. \tab\cr \code{cul76} \tab DNA\tab Not tested
 with experimental \tab Cullen and Bick, 1976\cr \tab\tab results. \tab\cr
 \code{esc80} \tab DNA\tab Not tested with experimental \tab Escara and
 Hutton, 1980\cr \tab\tab results. \tab\cr \code{mus80} \tab DNA\tab Not
 tested with experimental \tab Musielski et al., 1981 \cr \tab\tab results.
 \tab }
}

\section{Formamide corrections}{
 \tabular{llll}{ \strong{Correcion} \tab
 \strong{Type} \tab \strong{Limits.Remarks}\tab \strong{Reference} \cr
 \code{bla96} \tab DNA\tab With formamide concentration\tab Blake, 1996 \cr
 \tab\tab in mol/L. \tab \cr \code{lincorr} \tab DNA\tab With a % of
 formamide volume. \tab McConaughy et al., 1969;\cr \tab\tab \tab Record,
 1967; Casey and \cr \tab\tab \tab Davidson, 1977; Hutton, 1977 }
}

\examples{

}
\references{
\insertRef{marmur_determination_1962}{rmelting}

\insertRef{schildkraut_dependence_1965}{rmelting}

\insertRef{record_electrostatic_1967}{rmelting}

\insertRef{mcconaughy_nucleic_1969}{rmelting}

\insertRef{owen_determination_1969}{rmelting}

\insertRef{frank-kamenetskii_simplification_1971}{rmelting}

\insertRef{britten_analysis_1974}{rmelting}

\insertRef{cullen_thermal_1976}{rmelting}

\insertRef{hutton_renaturation_1977}{rmelting}

\insertRef{casey_rates_1977}{rmelting}

\insertRef{hall_evolution_1980}{rmelting}

\insertRef{escara_thermal_1980}{rmelting}

\insertRef{musielski_influence_1981}{rmelting}

\insertRef{freier_improved_1986}{rmelting}

\insertRef{breslauer_predicting_1986}{rmelting}

\insertRef{wahl_molecular_1987}{rmelting}

\insertRef{wetmur_dna_1991}{rmelting}

\insertRef{chester_dimethyl_1993}{rmelting}

\insertRef{sugimoto_rna/dna_1994}{rmelting}

\insertRef{sugimoto_thermodynamic_1995}{rmelting}

\insertRef{santalucia_improved_1996}{rmelting}

\insertRef{sugimoto_improved_1996}{rmelting}

\insertRef{blake_thermodynamic_1996}{rmelting}

\insertRef{blake_denaturation_1996}{rmelting}

\insertRef{mitsuhashi_technical_1996}{rmelting}

\insertRef{allawi_thermodynamics_1997}{rmelting}

\insertRef{santalucia_unified_1998}{rmelting}

\insertRef{xia_thermodynamic_1998}{rmelting}

\insertRef{allawi_thermodynamics_1998}{rmelting}

\insertRef{blake_thermal_1998}{rmelting}

\insertRef{allawi_nearest_1998}{rmelting}

\insertRef{allawi_nearest-neighbor_1998}{rmelting}

\insertRef{mathews_expanded_1999}{rmelting}

\insertRef{peyret_nearest-neighbor_1999}{rmelting}

\insertRef{peyret_prediction_2000}{rmelting}

\insertRef{bommarito_thermodynamic_2000}{rmelting}

\insertRef{kawakami_thermodynamic_2001}{rmelting}

\insertRef{von_ahsen_oligonucleotide_2001}{rmelting}

\insertRef{le_novere_melting_2001}{rmelting}

\insertRef{ohmichi_long_2002}{rmelting}

\insertRef{santalucia_thermodynamics_2004}{rmelting}

\insertRef{tanaka_thermodynamic_2004}{rmelting}

\insertRef{mctigue_sequence-dependent_2004}{rmelting}

\insertRef{owczarzy_effects_2004}{rmelting}

\insertRef{broda_thermodynamic_2005}{rmelting}

\insertRef{watkins_nearest-neighbor_2005}{rmelting}

\insertRef{asanuma_clear-cut_2005}{rmelting}

\insertRef{otoole_stability_2005}{rmelting}

\insertRef{lu_set_2006}{rmelting}

\insertRef{kierzek_nearest_2006}{rmelting}

\insertRef{tan_nucleic_2006}{rmelting}

\insertRef{otoole_comprehensive_2006}{rmelting}

\insertRef{tan_rna_2007}{rmelting}

\insertRef{wright_nearest_2007}{rmelting}

\insertRef{davis_thermodynamic_2007}{rmelting}

\insertRef{blose_non-nearest-neighbor_2007}{rmelting}

\insertRef{badhwar_thermodynamic_2007}{rmelting}

\insertRef{davis_thermodynamic_2008}{rmelting}

\insertRef{miller_thermodynamic_2008}{rmelting}

\insertRef{owczarzy_predicting_2008}{rmelting}

\insertRef{dumousseau_melting_2012}{rmelting}
}