Document Detail


uAnalyze: Web-Based High Resolution DNA Melting Analysis with Comparison to Thermodynamic Predictions.
MedLine Citation:
PMID:  22889837     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
uAnalyze ^{SM} 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 is 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 +/- SD of the difference between experimental and predicted fluorescence at 50% helicity was -0.04 +/- 0.48°C. uAnalyze requires Flash, is not browser specific and can be accessed at http://www.dna.utah.edu/uv/uanalyze.html.
Authors:
Zachary L Dwight; Robert Palais; Carl T Wittwer
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-8-9
Journal Detail:
Title:  IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM     Volume:  -     ISSN:  1557-9964     ISO Abbreviation:  IEEE/ACM Trans Comput Biol Bioinform     Publication Date:  2012 Aug 
Date Detail:
Created Date:  2012-8-14     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101196755     Medline TA:  IEEE/ACM Trans Comput Biol Bioinform     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
University of Utah, Salt Lake City.
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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