DINAMelt web server for nucleic acid melting prediction

DINAMelt web server for nucleic acid melting prediction

2005 | Nicholas R. Markham and Michael Zuker
The DINAMelt web server predicts the melting behavior of single-stranded nucleic acids in solution, providing equilibrium melting profiles as a function of temperature. It calculates the free energy, enthalpy, entropy, and heat capacity of the system, as well as UV absorbance, for various molecular species. The server considers both homodimers and heterodimers, and allows for non-complementary strands and unequal concentrations. It accounts for competition among molecular species and computes probabilities of base pairing and folding. The server also provides UV absorbance, heat capacity, and concentration plots, and allows users to download text files with calculated data. The server is connected to an active research program and is expected to evolve with new theories and software. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/. The server supports both simple and advanced input forms, allowing users to submit sequences, temperature ranges, and salt conditions. It also provides output in text and graphical formats, including concentration, heat capacity, and absorbance plots. The server is designed to handle a variety of nucleic acid types, including DNA and RNA, and allows for the calculation of multiple melting temperatures based on different criteria. The server is supported by IBM Research and has been used in collaboration with IDT to validate its predictions against experimental data. The server is cited as a general reference, with additional articles for citation related to its algorithms and energy parameters. The server is available for download in various formats, and the authors acknowledge funding from the National Institutes of Health and private RPI funds.The DINAMelt web server predicts the melting behavior of single-stranded nucleic acids in solution, providing equilibrium melting profiles as a function of temperature. It calculates the free energy, enthalpy, entropy, and heat capacity of the system, as well as UV absorbance, for various molecular species. The server considers both homodimers and heterodimers, and allows for non-complementary strands and unequal concentrations. It accounts for competition among molecular species and computes probabilities of base pairing and folding. The server also provides UV absorbance, heat capacity, and concentration plots, and allows users to download text files with calculated data. The server is connected to an active research program and is expected to evolve with new theories and software. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/. The server supports both simple and advanced input forms, allowing users to submit sequences, temperature ranges, and salt conditions. It also provides output in text and graphical formats, including concentration, heat capacity, and absorbance plots. The server is designed to handle a variety of nucleic acid types, including DNA and RNA, and allows for the calculation of multiple melting temperatures based on different criteria. The server is supported by IBM Research and has been used in collaboration with IDT to validate its predictions against experimental data. The server is cited as a general reference, with additional articles for citation related to its algorithms and energy parameters. The server is available for download in various formats, and the authors acknowledge funding from the National Institutes of Health and private RPI funds.
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