uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application

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Publication Type Manuscript
School or College School of Medicine
Department Pathology
Creator Dwight, Zachary Lawrence
Other Author Palais, Robert; Wittwer, Carl T.
Title uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application
Date 2011
Description uMeltSM is a flexible web-based tool for predicting DNA melting curves and denaturation profiles of PCR products. The user defines an amplicon sequence and chooses a set of thermodynamic and experimental parameters that include nearest-neighbor stacking energies, loop entropy effects, cation (monovalent and Mg++) concentrations and a temperature range. Using an accelerated partition function algorithm along with chosen parameter values, uMelt interactively calculates and visualizes the mean helicity and the dissociation probability at each sequence position at temperatures within the temperature range. Predicted curves display the mean helicity as a function of temperature or as derivative plots. Predicted profiles display stability as a function of sequence position either as 50% helicity temperatures or as the helicity probability at specific temperatures. The loss of helicity associated with increasing temperature may be viewed dynamically to visualize domain formation within the molecule. Results from fluorescent high-resolution melting experiments match the number of predicted melting domains and their relative temperatures. However, the absolute melting temperatures vary with the selected thermodynamic parameters and current libraries do not account for the rapid melting rates and helix stabilizing dyes used in fluorescent melting experiments. uMelt provides a convenient platform for simulation and design of high-resolution melting assays.
Type Text
Publisher Oxford University Press
DOI 10.1093/bioinformatics/btr065
Language eng
Bibliographic Citation Dwight, Z. L., Palais, R., & Wittwer, C. T. (2011). uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Bioinformatics, 27(7), 1019-20.
Rights Management © Oxford University Press. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version Dwight, Z. L., Palais, R., & Wittwer, C. T. (2011). uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Bioinformatics, 27(7), 1019-20 is available online at: doi:10.1093/bioinformatics/btr065.
Format Medium application/pdf
Format Extent 203,433 bytes
Identifier ir-main,17007
ARK ark:/87278/s615514n
Setname ir_uspace
Date Created 2012-06-13
Date Modified 2012-06-13
ID 702398
Reference URL https://collections.lib.utah.edu/ark:/87278/s615514n
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