Biology:Comparison of DNA melting prediction software

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This comparison of DNA melting prediction software includes source code and web based software for predicting DNA melting and structure.

Software types, methods, availability, etc.

Name	Links	Distinguishing features	Method	Language	Seq limit	Dissociation
DNAmelt	source code		Stat mech	MATLAB	1 Mb	?
MeltSim 1.0	source code	GUI for Windows	Stat mech	Pascal Delphi	2 Mb	?
MeltSim 1.99	source code	CLI	Stat mech	C		?
Poland server	webserver		Stat mech	F77	1 kb	Yes
Stitchprofiles.uio.no	webserver		Stat mech	Perl, gnuplot	480 kb	No
uMelt	webserver		Stat mech	Adobe Flex	3500 b	?
WebSIDD	webserver		Stat mech	C++	10 kb	?
OligoCalc	webserver
OligoAnalyzer 3.1	webserver

NN = Methods using nearest neighbor thermodynamic parameters for predicting oligonucleotide melting temperatures (T_m), melting curves, DSC curves or other properties derived from the law of mass action.

Stat mech = Statistical mechanical methods applied to longer DNA molecules to predict melting processes with intermediate subtransitions. Melting profiles are computed based on partition functions that account for the partially melted DNA configurations.

Supported input features

Name	NA types				Concentration			Thermodynamic parameters	Other input
	Lin DNA	circ DNA	RNA	LNA	[Na+]	[Mg++]	Strand conc.
DNAmelt	Yes	No	No	No	?	?	?	?
GeneFizz	Yes	No	No	No	No	No	No	No	EMBL/Genbank file
MeltSim	Yes	No	No	No	Yes	No	No	Yes
Poland server	Yes	No	Yes	No	No	No	Yes	Yes	mismatches
Stitchprofiles.uio.no	Yes	No	No	No	Yes	No	No	Yes	helicities
uMelt	Yes	No	No	No	Yes	Yes	No	Yes
WebSIDD	Yes	Yes	No	No	No	No	No	No	Stress level

Supported output features

Name	Melting curves		Probability functions	Contour lines (meltmap)		Other output
	Θ(T)	dΘ/dT	bp	50%	Other %
DNAmelt	?	?	Yes	?	?
GeneFizz	No	No	Yes	No	No	displays CDS, gene, mRNA
MeltSim	?	Yes	Yes	Yes	No
Poland server	?	Yes	Yes	Yes	No	gel mobility
Stitchprofiles.uio.no	Yes	No	Yes	Yes	Yes	stitch profiles, FF parameters
uMelt	Yes	Yes	No	Yes	No	dynamic melting profile
WebSIDD	No	No	Yes	No	No	G(x), B-Z probabilities, # open bp, # open regions, minimum E

External links

• bioinformatics.org/Meltsim
• Poland service (Düsseldorf)
• Stitchprofiles.uio.no
• uMelt: Melting Curve Prediction
• GeneFizz server
• WebSIDD and SIBZ
• DNA thermodynamics calculations - T_m, melting profile, mismatches, free energy calculations

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