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
- 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.
- Michoel, T; Van de Peer, Y (2006). "Helicoidal transfer matrix model for inhomogeneous DNA melting". Phys Rev E Stat Nonlin Soft Matter Phys. 73: 011908. doi:10.1103/PhysRevE.73.011908. PMID 16486186.
- A windowing approach is used for sequences > 1Mb
- 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: 370–5. doi:10.1093/bioinformatics/15.5.370. PMID 10366657.
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External links
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