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 |
ID |
709213 |
Reference URL |
https://collections.lib.utah.edu/ark:/87278/s6th95js |