	MELTING 5 help
		
More information is available in the user-guide. Type `man melting' to access it or consult one of the 
melting.xxx files, where xxx states for ps (postscript), pdf or html.
		
	Information about MELTING 5 : 

-h
	Displays this help and quit. 
	
-L
	Displays legal information and quit.
	 
-V
	Print the version number. 

-p
	Return path where to find the calorimetric tables. 


	Mandatory options :

-S [sequence]
	Nucleic acid sequence, mandatory. The sens of this sequence must be 5'-3'.


-C [complementary sequence]
	Nucleic acid complementary sequence, mandatory only if there is inosine bases or azobenznes in the sequence entered with the opton -S. The sens of this sequence must be 3'-5''.

-E [agent1=concentration1:agent2=concentration2]
	Different agent concentrations in the solution. The agents can be cations (Na, K, Tris, Mg for Na+, K+, Tris+ and Mg2+), dNTP or other agents (DMSO, formamide). The concentrations must be in Mol/L but there are some exceptions : DMSO is a percentage, formamide is a percentage if the method lincorr is chosen and in Mol/L if the method bla96 is chosen. At least one cation concentration is mandatory, the other agents are optional. See the documentation for the concentration limits. It depends on the used correction.

-P [nucleotide concentration]
	Concentration in mol/L of the nucleic acid strand in excess, mandatory.

-H [hybridization]
	Type of hybridization, mandatory. Four types of hybridization are allowed : dnadna (DNA duplex), rnarna (RNA duplex), dnarna or rnadna (hybrid DNA/RNA) and mrnarna or rnamrna (2-o-methyl RNA/ RNA). The type of hybridization defines the kind of the sequence and its complementary. 
		Ex : dnarna = the sequence (entered with the option -S) is a DNA sequence and its complementary (entered with the option -C) is a RNA sequence.
		Ex : rnadna = the sequence (entered with the option -S) is a RNA sequence and its complementary (entered with the option -C) is a DNA sequence  


	General options :

-v
	Switch ON the verbose mode, issuing lot more info. Default is OFF.

-T [threshold value]
	Threshold for approximative computation. Default is 60.

-nnpath [folder pathway]
	Change the default pathway (Data) where to find the default calorimetric tables (thermodynamic parameters).

-O [filename]
	To write the results in an output file. filename is the name or the pathway of the file.

-self
	To precise that the sequence entered with the option -S is self complementary. No complementary sequence is mandatory. The program automatically can detect a self complementary sequence for perfect matching sequences or sequences with dangling ends. In these cases, the option -self is not necessary, otherwise we need to precise that the sequences are self complementary.

-F [factor value]
	Correction for the concentration of nucleic acid. F is automatically 1 if the sequences are self complementary. Otherwise F is 4 if the both strands are present in equivalent amount and 1 if one strand is in excess. The default factor value is 4.

	Set of thermodynamic parameters and methods : 
By default, the approximative mode is used for oligonucleotides longer than 60 bases (the default threshold value), otherwise the nearest 
neighbor model is used. 

-am [optional name]
	Forces to use a specific approximative formula. You can use one of the following : 
		(DNA)
			ahs01 (from von Ahsen et al. 2001)
			che93 (from Marmur 1962, Chester et al. 1993)
			che93corr (from von Ahsen et al. 2001, Marmur 1962, Chester et al. 1993)
			schdot (Marmur-Schildkraut-Doty formula)
			owe69 (from Owen et al. 1969)
			san98 (from Santalucia et al. 1998)
			wetdna91 (from Wetmur 1991)  (by default)
		(RNA)
			wetrna91 (from Wetmur 1991)  (by default) 
		(DNA/RNA)
			wetdnarna91 (from Wetmur 1991)  (by default)
	If there is no formula name after the option -am, we will compute the melting temperature with the default approximative formula. 

-nn [optional name]
	Forces to use a specific nearest neighbor model. You can use one of the following : 
		(DNA)
			all97 (from Allawi and Santalucia 1997) (by default)
			bre86 (from Breslauer et al. 1986)
			san04 (from Hicks and Santalucia 2004)  
			san96 (from Santalucia et al. 1996)
			sug96 (from Sugimoto et al 1996)
			tan04 (from Tanaka et al. 2004)
		(RNA)
			fre86 (from Freier al. 1986)
			xia98 (from Xia et al. 1998)  (by default)
		(DNA/RNA)
			sug95 (from Sugimoto et al. 1995)  (by default)
		(mRNA/RNA)
			tur06 (from Kierzek et al. 2006)  (by default)

	If there is no formula name after the option -nn, we will compute the melting temperature with the default nearest neighbor model. 
	Each nearest neighbor model uses a specific xml file containing the thermodynamic values. If you want to use another file, write the file name or the file pathway preceded by ':' (-nn [optionalname:optionalfile]).
		Ex : -nn tan04:fileName if you want to use the nearest neighbor model from Tanaka et al. 2004 with the thermodynamic parameters in the file fileName. 
		Ex : -nn :fileName if you want to use the default nearest neighbor model with the thermodynamic parameters in the file fileName. 

-sinMM [name]
	Forces to use a specific nearest neighbor model for single mismatch(es) in the sequences. You can use one of the following :
		(DNA)
			allsanpey (from Allawi, Santalucia and Peyret 1997, 1998 and 1999)  (by default)
	    (DNA/RNA)
        	wat10 (from Watkins et al. 2011) (by default)
		(RNA)
			tur06 (from Lu et al. 2006)
			zno07 (from Davis et al. 2007)  (by default)
			zno08 (from Davis et al. 2008)

	To change the file containing the thermodynamic parameters for single mismatch computation, the same syntax as the one for the -nn option is used.

-GU [name]
	Forces to use a specific nearest neighbor model for GU base pairs in RNA sequences. You can use one of the following :
	       tur99 (from Turner et al. 1999).
	       ser12 (from Serra et al. 2012) (by default)
	To change the file containing the thermodynamic parameters for GU base pairs computation, the same syntax as the one for the -nn option is used.

-tanMM [name]
	Forces to use a specific nearest neighbor model for tandem mismatches in the sequences. You can use one of the following :
		(DNA)
			allsanpey (from Allawi, Santalucia and Peyret 1997, 1998 and 1999)  (by default)
		(RNA)
			tur99 (from Mathews et al. 1999)  (by default)

	To change the file containing the thermodynamic parameters for tandem mismatches computation, the same syntax as the one for the -nn option is used. 

-intLP [name]
	Forces to use a specific nearest neighbor model for internal loop in the sequences. You can use one of the following :
		(DNA)
			san04 (from Hicks and Santalucia 2004)  (by default)
		(RNA)
			tur06 (from Lu et al. 2006)  (by default)
			zno07 (from Badhwarr et al. 2007, only for 1x2 loop)

	To change the file containing the thermodynamic parameters for internal loop computation, the same syntax as the one for the -nn option is used.

-sinDE [name]
	Forces to use a specific nearest neighbor model for single dangling end(s) in the sequences. You can use one of the following :
		(DNA)
			bom00 (from Bommarito et al. 2000)  (by default)
			sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
		(RNA)
			sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
			ser08 (from Miller et al. 2008)  (by default)

	To change the file containing the thermodynamic parameters for single dangling end computation, the same syntax as the one for the -nn option is used. 

-secDE [name]
	Forces to use a specific nearest neighbor model for second dangling end(s) in the sequences. You can use one of the following :
		(DNA)
			sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends)  (by default)
		(RNA)
			sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)
			ser05 (from O'toole et al. 2005)
			ser06 (from O'toole et al. 2006)  (by default)

	To change the file containing the thermodynamic parameters for second dangling end computation, the same syntax as the one for the -nn option is used. 

-lonDE [name]
	Forces to use a specific nearest neighbor model for long dangling end(s) in the sequences (self complementary sequences). You can use one of the following :
		(DNA)
			sugdna02 (from Ohmichi et al. 2002, only for polyA dangling ends)  (by default)
		(RNA)
			sugrna02 (from Ohmichi et al. 2002, only for polyA dangling ends)  (by default)

	To change the file containing the thermodynamic parameters for long dangling end computation, the same syntax as the one for the -nn option is used. 

-sinBU [name]
	Forces to use a specific nearest neighbor model for single bulge loop(s) in the sequences. You can use one of the following :
		(DNA)
			san04 (from Hicks and Santalucia 2004)
			tan04 (from Tanaka et al. 2004)  (by default)
		(RNA)
			ser07 (from Blose et al. 2007)
			tur06 (from Lu et al. 1999 and 2006)  (by default)

	To change the file containing the thermodynamic parameters for single bulge loop computation, the same syntax as the one for the -nn option is used. 

-lonBU [name]
	Forces to use a specific nearest neighbor model for long bulge loop(s) in the sequences. You can use one of the following :
		(DNA) 
			san04 (from Hicks and Santalucia 2004)  (by default)
		(RNA)
			tur06 (from Mathews et al. 1999 and Lu et al 2006)  (by default)
			
	To change the file containing the thermodynamic parameters for long bulge loop computation, the same syntax as the one for the -nn option is used. 

-CNG [name]
	Forces to use a specific nearest neighbor model for RNA sequences composed of CNG repeats (G(CNG)xC where N is a single N/N mismatch). You can only use bro05 (from Magdalena et al. 2005).
	To change the file containing the thermodynamic parameters for RNA sequences composed of CNG repeats computation, the same syntax as the one for the -nn option is used. 

-ino [name]
	Forces to use a specific nearest neighbor model for inosine base (I) in the sequences. You can use one of the following :
		(DNA)
			san05 (from Watkins and Santalucia 2005)  (by default)
		(RNA)
			zno07 (from Wright et al. 2007)  (by default)
			
	To change the file containing the thermodynamic parameters for inosine base computation, the same syntax as the one for the -nn option is used. 

-ha [name]
	Forces to use a specific nearest neighbor model for hydroxyadenine base (A*) in DNA sequences. You can only use sug01 (from Kawakami et al. 2001).
	To change the file containing the thermodynamic parameters for hydroxyadenine base computation, the same syntax as the one for the -nn option is used. 

-azo [name]
	Forces to use a specific nearest neighbor model for DNA sequences containing azobenzene (cis : X_C or trans : X_T). You can only use asa05 (from Asanuma et al. 2005).
	To change the file containing the thermodynamic parameters for azobenzene computation, the same syntax as the one for the -nn option is used.

-lck [name]
	Forces to use a specific nearest neighbor model for DNA sequences containing locked nucleic acid (Al, Tl, Cl or Gl). You can use mct04 (from McTigue et al. 2004) or
	owc11 (from Owczarzy et al. 2011, by default).
	To change the file containing the thermodynamic parameters for locked acid nucleic computation, the same syntax as the one for the -nn option is used.

-tanLck [name]
	Forces to use a specific nearest neighbor model for DNA sequences containing consecutive locked nucleic acid (Al, Tl, Cl or Gl). You can only use owc11 (from Owczarzy et al. 2011, by default).
	To change the file containing the thermodynamic parameters for locked acid nucleic computation, the same syntax as the one for the -nn option is used.

-sinMMLck [name]
	Forces to use a specific nearest neighbor model for DNA sequences containing consecutive locked nucleic acid with one single mismatch (Al, Tl, Cl or Gl).
	You can use only owc11 (from Owczarzy et al. 2011, by default).
	To change the file containing the thermodynamic parameters for locked acid nucleic computation, the same syntax as the one for the -nn option is used.
               
	Set of melting temperature corrections

-ion [name]
	Forces to use a specific ion correction. You can use one of the following corrections : 
	Sodium corrections :
		(DNA)
			ahs01 (from von Ahsen et al. 2001)
			kam71 (from Frank-Kamenetskii et al 2001)
			owc1904 (equation 19 from Owczarzy et al. 2004)
			owc2004 (equation 20 from Owczarzy et al. 2004)
			owc2104 (equation 21 from Owczarzy et al. 2004)
			owc2204 (equation 21 from Owczarzy et al. 2004)  (by default)
			san96 (from Santalucia et al. 1996)
			san04 (from Santalucia et al. 1998, 2004)
			schlif (from Schildkraut and Lifson 1965)
			tanna06 (from Tan et al. 2006)
			wetdna91 (from Wetmur 1991)
		(RNA or 2-o methyl RNA)
			tanna07 (from Tan et al. 2007)  (by default)
			wetrna91 (from Wetmur 1991)
		(RNA/DNA)
			wetdnarna91 (from Wetmur 1991)  (by default)
	Magnesium corrections : 
		(DNA)
			owcmg08 (from Owczarzy et al. 2008)  (by default)
			tanmg06 (from Tan et al. 2006)
		(RNA or 2-o methyl RNA)
			tanmg07 (from Tan et al. 2007)  (by default)
	Mixed Na Mg corrections
		(DNA)
			owcmix08 (from Owczarzy et al. 2008)  (by default)
			tanmix07 (from Tan et al. 2007)
		(RNA or 2-o methyl RNA)
			tanmix07 (from Tan et al. 2007)  (by default)

	By default, the program use the algorithm from Owczarzy et al 2008 : ratio = Mg^0.5 and monovalent = Na + Tris + K
		if monovalent = 0, a magnesium correction is used.
		if ratio < 0.22, a sodium correction is used.
		if 0.22 <= ratio < 6, a mixed Na Mg correction is used.
		if ratio >= 6, a magnesium correction is used.

-naeq [name]
	Forces to use a specific ion correction which gives a sodium equivalent concentration if other cations are present. You can use one of the following :
		(DNA)
			ahs01 (from von Ahsen et al 2001)  (by default)
			mit96 (from Mitsuhashi et al. 1996)
			pey00 (from Peyret 2000) 

	For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.

-DMSO [name]
	Forces to use a specific DMSO correction (DMSO is always in percent). You can use one of the following : 
		(DNA)
			ahs01 (from von Ahsen et al 2001)  (by default)
			mus81 (from Musielski et al. 1981)
			cul76 (from Cullen et al. 1976)
			esc80 (from Escara et al. 1980). 

	For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.

-for [name]
	Forces to use a specific formamide correction. You can use one of the following : 
		(DNA)
			bla96 (from Blake et al 1996) with formamide concentration in mol/L  (by default)
			lincorr (linear correction) with a percent of formamide volume

	For the other types of hybridization, the DNA default correction is used but there is no guaranty of accuracy.
                                   