uAnalyze: web-based high-resolution DNA melting analysis with comparison to thermodynamic predictions

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Publication Type pre-print
School or College School of Medicine
Department Pathology
Creator Dwight, Zachary Lawrence
Other Author Palais, Robert; Wittwer, Carl T.
Title uAnalyze: web-based high-resolution DNA melting analysis with comparison to thermodynamic predictions
Date 2012-01-01
Description Abstract-uAnalyzeSM is a web-based tool for analyzing high-resolution melting data of PCR products. PCR product sequence is input by the user and recursive nearest neighbor thermodynamic calculations used to predict a melting curve similar to uMELT (http://www.dna.utah.edu/umelt/umelt.html). Unprocessed melting data are input directly from LightScanner-96, LS32, or HR-1 data files or via a generic format for other instruments. A fluorescence discriminator identifies low intensity samples to prevent analysis of data that cannot be adequately normalized. Temperature regions that define fluorescence background are initialized by prediction and optionally adjusted by the user. Background is removed either as an exponential or by linear baseline extrapolation. The precision or, "curve spread," of experimental melting curves is quantified as the average of the maximum helicity difference of all curve pairs. Melting curve accuracy is quantified as the area or "2D offset" between the average experimental and predicted melting curves. Optional temperature overlay (temperature shifting) is provided to focus on curve shape. Using 14 amplicons of CYBB, the mean þ= standard deviation of the difference between experimental and predicted fluorescence at 50 percent helicity was 0:04 þ = 0:48C. uAnalyze requires Flash, is not browser specific and can be accessed at http://www.dna.utah.edu/uv/uanalyze.html.
Type Text
Publisher Institute of Electrical and Electronics Engineers (IEEE)
Volume 9
Issue 6
First Page 1805
Last Page 1811
Language eng
Bibliographic Citation Dwight, Z. L., Palais, R., & Wittwer, C. T. (2012). uAnalyze: web-based high-resolution DNA melting analysis with comparison to thermodynamic predictions. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 9(6), 1805-11.
Rights Management (c) 2012 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
Format Medium application/pdf
Format Extent 705,186 bytes
Identifier uspace,18313
ARK ark:/87278/s6th95js
Setname ir_uspace
Date Created 2013-08-13
Date Modified 2013-08-20
ID 709213
Reference URL https://collections.lib.utah.edu/ark:/87278/s6th95js
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