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Open Access Highly Accessed Research article

pcrEfficiency: a Web tool for PCR amplification efficiency prediction

Izaskun Mallona*, Julia Weiss and Marcos Egea-Cortines

Author Affiliations

Genetics, Institute of Plant Biotechnology (IBV), Technical University of Cartagena (UPCT), Campus Muralla del Mar, 30202 Cartagena, Spain

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BMC Bioinformatics 2011, 12:404  doi:10.1186/1471-2105-12-404

Published: 20 October 2011

Additional files

Additional file 1:

Data overview. Data comprise 90 different amplification products that included different template sources. Efficiencies ranged between 1 (no amplification) and 2 (perfect exponential duplication). Measured parameters contained: complete amplicon length (lengthSequence), primer length (forLength and revLength, for the forward and reverse primers respectively), G+C content of amplicon and primers (gcSequence and gcPrimers), logical variables showing the presence of N6 or above repeats (aRepeats, tRepeats, cRepeats, gRepeats); and aCount, tCount, cCount, gCount integer variables regarding the length of the longest repeat found), primer melting temperature (tmForward, tmReverse), tendency to form primer dimers (primerDimers), tendency to selfcomplementarity (primersSelfcom), and the 3' terminal two nucleotides of each primer (trap3For, trap3Rev) as well the terminal last nucleotides of each primer (trap3LastFor, trap3LastRev). Metadata for each PCR reaction included the thermocycler used (machine), sample origin (i.e. genomic or cDNA; template) and organ involved (source), person involved (operator), species (species) and line or variety (var), presence of palindromes at the amplicon (sequencePalindromes), primer length (primersLength), and PCR efficiency (efficiency).

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Additional file 2:

Post-hoc categorical variable analysis. The variables regarding PCR template (GD, genomic; CD, cDNA; plasmid, Escherichia coli plasmid; yGD, yeast genomic) and 3' primer termini (U, purine; Y, pyrimidine) were analyzed by asymptotic Wilcoxon Mann-Whitney rank sum tests (Z, Z value; p, p-value), and the effect sizes estimated by the two tailed p-value (Cohen's d, mean difference; Hedge's g, unbiased estimate of d; r, correlation coefficient; and n, the total sample size, which is twice the effective sample size when the termini of the two oligos are analyzed).

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