PcrEfficiency: A Web tool for PCR amplification efficiency prediction

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Mallona, Izaskun ^a   Weiss, Julia ^a   Marcos, Egea Cortines ^a  

^a TECHNICAL UNIVERSITY OF CARTAGENA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLIFICATION EFFICIENCIES; DIFFERENTIAL GENE EXPRESSIONS; GENERALIZED ADDITIVE MODEL; PCR AMPLIFICATION; QUANTITATIVE PCR; QUANTITATIVE REAL TIME PCR; STATISTICAL APPROACH; WEB-BASED SERVICE;

EXPERIMENTS; GENE EXPRESSION; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; TOOLS;

EFFICIENCY;

BACTERIA (MICROORGANISMS);

PRIMER DNA;

ARTICLE; BACTERIUM; COMPUTER PROGRAM; GENETICS; HUMAN; INTERNET; METHODOLOGY; PLANT; POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; STATISTICAL MODEL;

BACTERIA; DNA PRIMERS; HUMANS; INTERNET; MODELS, STATISTICAL; PLANTS; POLYMERASE CHAIN REACTION; REAL-TIME POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 80054716265     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-404     Document Type: Article

References (41)

1. Higuchi R, Fockler C, Dollinger G, Watson R. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Nature Biotechnology 1993, 11(9):1026-1030.
2. Luu-The V, Paquet N, Calvo E, Cumps J. Improved real-time RT-PCR method for high-throughput measurements using second derivative calculation and double correction. Biotechniques 2005, 38(2):287-293. 10.2144/05382RR05, 15727135.
3. Bustin S, Benes V, Garson J, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl M, Shipley G, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry 2009, 55(4):611. 10.1373/clinchem.2008.112797, 19246619.
4. Morrison T, Weis J, Wittwer C. Quantification of low-copy transcripts by continuous SYBR® Green I monitoring during amplification. Biotechniques 1998, 24(6):954-962.
5. Livak K, Schmittgen T. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C (T)) method. Methods 2001, 25(4):402-408. 10.1006/meth.2001.1262, 11846609.
6. Ramakers C, Ruijter J, Deprez R, Moorman A. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neuroscience Letters 2003, 339:62-66. 10.1016/S0304-3940(02)01423-4, 12618301.
7. Monod J. The growth of bacterial cultures. Annual Reviews in Microbiology 1949, 3:371-394.
8. Schefe J, Lehmann K, Buschmann I, Unger T, Funke-Kaiser H. Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's CT difference" formula. Journal of Molecular Medicine 2006, 84(11):901-910. 10.1007/s00109-006-0097-6, 16972087.
9. Tichopad A, Dilger M, Schwarz G, Pfaffl M. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Research 2003, 31(20):e122. 10.1093/nar/gng122, 219490, 14530455.
10. Qu W, Shen Z, Zhao D, Yang Y, Zhang C. MFEprimer: multiple factor evaluation of the specificity of PCR primers. Bioinformatics 2009, 25(2):276. 10.1093/bioinformatics/btn614, 19038987.
11. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. Journal of Molecular Biology 1962, 5:109. 10.1016/S0022-2836(62)80066-7, 14470099.
12. Wallace R, Shaffer J, Murphy R, Bonner J, Hirose T, Itakura K. Hybridization of synthetic oligodeoxyribonucleotides to ΦX174 DNA: the effect of single base pair mismatch. Nucleic Acids Research 1979, 6(11):3543. 10.1093/nar/6.11.3543, 327955, 158748.
13. Howley P, Israel M, Law M, Martin M. A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. Journal of Biological Chemistry 1979, 254(11):4876.
14. Breslauer K, Frank R, Blöcker H, Marky L. Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Sciences 1986, 83(11):3746.
15. Manchado-Rojo M, Weiss J, Egea-Cortines M. Using 23s rDNA to identify contaminations of Escherichia coli in Agrobacterium tumefaciens cultures. Analytical Biochemistry 2008, 372(2):253-254. 10.1016/j.ab.2007.09.011, 17945175.
16. Weiss J, Egea-Cortines M. Transcriptomic analysis of cold response in tomato fruits identifies dehydrin as a marker of cold stress. Journal of Applied Genetics 2009, 50(4):311-319. 10.1007/BF03195689, 19875881.
17. Mallona I, Lischewski S, Weiss J, Egea-Cortines M. Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biology 2010, 10:4. 10.1186/1471-2229-10-4, 2827423, 20056000.
18. Delgado-Benarroch L, Weiss J, Egea-Cortines M. The mutants compacta ähnlich, Nitida and Grandiflora define developmental compartments and a compensation mechanism in floral development in Antirrhinum majus. Journal of Plant Research 2009, 122(5):559-569. 10.1007/s10265-009-0236-6, 19412653.
19. Mallona I, Egea-Cortines M, Weiss J. Conserved and divergent expression rhythms of CAM related and core clock genes in the Cactus Opuntia ficus-indica. Plant Physiology 2011, 156(4):1978-1989. 10.1104/pp.111.179275, 21677095., http://www.plantphysiol.org/content/early/2011/06/15/pp.111.179275.abstract
20. Hothorn T, Hornik K, van de Wiel M, Zeileis A. coin: Conditional Inference Procedures in a Permutation Test Framework. R package version 0.6-6 2006, , http://CRAN.R-project.org
21. Wood S. mgcv: GAMs and generalized ridge regression for R. Future 2001, 1:20.
22. Wood S. Stable and efficient multiple smoothing parameter estimation for generalized additive models. Journal of the American Statistical Association 2004, 99(467):673-686.
23. Akaike H. A new look at the statistical model identification. IEEE Transactions on Automatic Control 1974, 19(6):716-723.
24. Davis J, Goadrich M. The relationship between Precision-Recall and ROC curves. Proceedings of the 23rd International Conference on Machine Learning, ACM 2006, 233-240.
25. Chapman B, Chang J. Biopython: Python tools for computational biology. ACM SIGBIO Newsletter 2000, 20(2):19.
26. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 2000, 132(3):365-386.
27. Rice P, Longden I, Bleasby A, et al. EMBOSS: the European molecular biology open software suite. Trends in Genetics 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
28. Chavali S, Mahajan A, Tabassum R, Maiti S, Bharadwaj D. Oligonucleotide properties determination and primer designing: a critical examination of predictions. Bioinformatics 2005, 21(20):3918. 10.1093/bioinformatics/bti633, 16105896.
29. Mann T, Humbert R, Dorschner M, Stamatoyannopoulos J, Noble WS. A thermodynamic approach to PCR primer design. Nucleic Acids Research 2009, 37(13):e95. 10.1093/nar/gkp443, 2715258, 19528077., http://nar.oxfordjournals.org/cgi/content/abstract/37/13/e95
30. Andreson R, Mols T, Remm M. Predicting failure rate of PCR in large genomes. Nucleic Acids Research 2008, 36(11):e66. 10.1093/nar/gkn290, 2441781, 18492719., http://nar.oxfordjournals.org/cgi/content/abstract/36/11/e66
31. Pierce K, Sanchez J, Rice J, Wangh L. Linear-After-The-Exponential (LATE)-PCR: Primer design criteria for high yields of specific single-stranded DNA and improved real-time detection. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(24):8609. 10.1073/pnas.0501946102, 1150831, 15937116.
32. Baskaran N, Kandpal R, Bhargava A, Glynn M, Bale A, Weissman S. Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. Genome Research 1996, 6(7):633. 10.1101/gr.6.7.633, 8796351.
33. Varadaraj K, Skinner D. Denaturants or cosolvents improve the specificity of PCR amplification of a G+ C-rich DNA using genetically engineered DNA polymerases. Gene (Amsterdam) 1994, 140:1-5.
34. Benita Y, Oosting R, Lok M, Wise M, Humphery-Smith I. Regionalized GC content of template DNA as a predictor of PCR success. Nucleic Acids Research 2003, 31(16):e99. 10.1093/nar/gng101, 169991, 12907751.
35. Tuomi J, Voorbraak F, Jones D, Ruijter J. Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value. Methods 2010, 50(4):313-322. 10.1016/j.ymeth.2010.02.003, 20138998.
36. Ritz C, Spiess A. qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis. Bioinformatics 2008, 24(13):1549. 10.1093/bioinformatics/btn227, 18482995.
37. Liu W, Saint D. A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics. Analytical Biochemistry 2002, 302:52-59. 10.1006/abio.2001.5530, 11846375.
38. R Development Core Team R: A Language and Environment for Statistical Computing 2008, R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], R Development Core Team., http://www.R-project.org
39. Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: Visualizing the performance of scoring classifiers 2009, [R package version 1.0-4]., http://CRAN.R-project.org/package=ROCR
40. Re AD. compute.es: Compute Effect Sizes 2010, [R package version 0.2]., http://CRAN.R-project.org/package=compute.es
41. Program NRA verification: Forecast verification utilities 2010, [R package version 1.31], Program NRA., http://CRAN.R-project.org/package=verification