Comparison of DNA melting prediction software

This comparison of DNA melting prediction software includes source code and web based software for predicting DNA melting and structure.[1]

Software types, methods, availability, etc.
Name Links Distinguishing features Method Language Seq limit Dissociation
DNAmelt[2] source code Stat mech MATLAB 1 Mb[3]  ?
MeltSim 1.0[4] source code GUI for Windows Stat mech Pascal Delphi 2 Mb  ?
MeltSim 1.99[4] 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 (Tm), 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

References and Notes
  1. Note: Not included in this comparison are software for RNA structure prediction, analysis of DNA microarray thermodynamics, nucleic acid design (e.g., primer design), and atomistic level simulations of DNA.
  2. Michoel, T; Van de Peer, Y (2006). "Helicoidal transfer matrix model for inhomogeneous DNA melting" (PDF). Physical Review E. 73 (1 Pt 1): 011908. doi:10.1103/PhysRevE.73.011908. hdl:20.500.11820/a07b9c30-0de6-4a6d-b3d9-9760260c5750. PMID 16486186. S2CID 13395867.
  3. A windowing approach is used for sequences > 1Mb
  4. Blake, RD; Bizzaro, JW; Blake, JD; Day, GR; Delcourt, SG; Knowles, J; Marx, KA; SantaLucia, J Jr (1999). "Statistical mechanical simulation of polymeric DNA melting with MELTSIM". Bioinformatics. 15 (5): 370–5. doi:10.1093/bioinformatics/15.5.370. PMID 10366657.
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