Table of Contents Author Guidelines Submit a Manuscript
Comparative and Functional Genomics
Volume 2012, Article ID 783138, 5 pages
http://dx.doi.org/10.1155/2012/783138
Research Article

Gemi: PCR Primers Prediction from Multiple Alignments

1Facultés de Médecine et de Pharmacie, Aix Marseille Université, URMITE, UM 63, CNRS 7278, INSERM, U1095, 13385 Marseille Cedex 05, France
2Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, IHU Méditerranée Infection, Centre Hospitalier-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, 13385 Marseille Cedex 05, France

Received 3 August 2012; Accepted 19 October 2012

Academic Editor: Brian Wigdahl

Copyright © 2012 Haitham Sobhy and Philippe Colson. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. I. M. Mackay, K. E. Arden, and A. Nitsche, “Real-time PCR in virology,” Nucleic Acids Research, vol. 30, no. 6, pp. 1292–1305, 2002. View at Google Scholar · View at Scopus
  2. J. M. Robertson and J. Walsh-Weller, “An introduction to PCR primer design and optimization of amplification reactions,” Methods in Molecular Biology, vol. 98, pp. 121–154, 1998. View at Google Scholar · View at Scopus
  3. P. E. Fournier and D. Raoult, “Prospects for the future using genomics and proteomics in clinical microbiology,” Annual Review of Microbiology, vol. 65, pp. 169–188, 2011. View at Google Scholar
  4. D. Raoult, P. E. Fournier, and M. Drancourt, “What does the future hold for clinical microbiology?” Nature Reviews Microbiology, vol. 2, no. 2, pp. 151–159, 2004. View at Publisher · View at Google Scholar · View at Scopus
  5. M. J. Espy, J. R. Uhl, L. M. Sloan et al., “Real-time PCR in clinical microbiology: applications for routine laboratory testing,” Clinical Microbiology Reviews, vol. 19, pp. 165–256, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. P. Colson, C. Tamalet, and D. Raoult, “SVARAP and aSVARAP: simple tools for quantitative analysis of nucleotide and amino acid variability and primer selection for clinical microbiology,” BMC Microbiology, vol. 6, article 21, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. D. A. Hysom, P. Naraghi-Arani, M. Elsheikh, A. C. Carrillo, P. L. Williams, and S. N. Gardner, “Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments,” PLoS One, vol. 7, Article ID e34560, 2012. View at Google Scholar
  8. C. Frech, K. Breuer, B. Ronacher, T. Kern, C. Sohn, and G. Gebauer, “Hybseek: pathogen primer design tool for diagnostic multi-analyte assays,” Computer Methods and Programs in Biomedicine, vol. 94, no. 2, pp. 152–160, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. S. N. Gardner, A. L. Hiddessen, P. L. Williams, C. Hara, M. C. Wagner, and B. W. Colston Jr., “Multiplex primer prediction software for divergent targets,” Nucleic Acids Research, vol. 37, no. 19, pp. 6291–6304, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. K. A. Abd-Elsalam, “Bioinformatic tools and guideline for PCR primer design,” African Journal of Biotechnology, vol. 2, no. 5, pp. 91–95, 2003. View at Google Scholar · View at Scopus
  11. H. Najafabadi, N. Torabi, and M. Chamankhah, “Designing multiple degenerate primers via consecutive pairwise alignments,” BMC Bioinformatics, vol. 9, article 55, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. H. S. Najafabadi, A. Saberi, N. Torabi, and M. Chamankhah, “MAD-DPD: designing highly degenerate primers with maximum amplification specificity,” BioTechniques, vol. 44, no. 4, pp. 519–526, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. R. Souvenir, J. Buhler, G. Stormo, and W. Zhang, “An iterative method for selecting degenerate multiplex PCR primers,” Methods in Molecular Biology, vol. 402, pp. 245–268, 2007. View at Publisher · View at Google Scholar · View at Scopus
  14. E. Gorrón, F. Rodríguez, D. Bernal et al., “A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes,” Bioinformatics, vol. 26, no. 16, pp. 2053–2054, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. A. Cornish-Bowden, “Nomenclature for incompletely specified bases in nucleic acid sequences: rcommendations 1984,” Nucleic Acids Research, vol. 13, no. 9, pp. 3021–3030, 1985. View at Publisher · View at Google Scholar · View at Scopus
  16. J. Marmur and P. Doty, “Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature,” Journal of Molecular Biology, vol. 5, pp. 109–118, 1962. View at Google Scholar · View at Scopus
  17. R. B. Wallace, J. Shaffer, R. F. Murphy, J. Bonner, T. Hirose, and K. Itakura, “Hybridization of synthetic oligodeoxyribonucleotides to φX 174 DNA: the effect of single base pair mismatch,” Nucleic Acids Research, vol. 6, no. 11, pp. 3543–3558, 1979. View at Publisher · View at Google Scholar · View at Scopus
  18. K. J. Breslauer, R. Frank, H. Blocker, and L. A. Marky, “Predicting DNA duplex stability from the base sequence,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 11, pp. 3746–3750, 1986. View at Google Scholar · View at Scopus
  19. S. Rozen and H. Skaletsky, “Primer3 on the WWW for general users and for biologist programmers,” Methods in Molecular Biology, vol. 132, pp. 365–386, 2000. View at Google Scholar · View at Scopus
  20. A. Untergasser, H. Nijveen, X. Rao, T. Bisseling, R. Geurts, and J. A. Leunissen, “Primer3Plus, an enhanced web interface to Primer3,” Nucleic Acids Research, vol. 35, pp. W71–W74, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. F. M. You, N. Huo, Y. Q. Gu et al., “BatchPrimer3: a high throughput web application for PCR and sequencing primer design,” BMC Bioinformatics, vol. 9, article 253, 2008. View at Publisher · View at Google Scholar · View at Scopus
  22. M. D. Gadberry, S. T. Malcomber, A. N. Doust, and E. A. Kellogg, “Primaclade—a flexible tool to find conserved PCR primers across multiple species,” Bioinformatics, vol. 21, no. 7, pp. 1263–1264, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. N. Kim and C. Lee, “QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments,” Bioinformatics, vol. 23, no. 17, pp. 2331–2333, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. N. Batnyam, J. Lee, J. Lee, S. Bok Hong, S. Oh, and K. Han, “UniPrimer: a web-based primer design tool for comparative analyses of primate genomes,” Comparative and Functional Genomics, vol. 2012, Article ID 520732, 8 pages, 2012. View at Publisher · View at Google Scholar
  25. A. L. Gervais, M. Marques, and L. Gaudreau, “PCRTiler: automated design of tiled and specific PCR primer pairs,” Nucleic Acids Research, vol. 38, no. 2, pp. W308–W312, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. S. Arvidsson, M. Kwasniewski, D. M. Riaño-Pachón, and B. Mueller-Roeber, “QuantPrime—a flexible tool for reliable high-throughput primer design for quantitative PCR,” BMC Bioinformatics, vol. 9, article 465, 2008. View at Publisher · View at Google Scholar · View at Scopus
  27. J. Ye, G. Coulouris, I. Zaretskaya, I. Cutcutache, S. Rozen, and T. Madden, “Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction,” BMC Bioinformatics, vol. 13, article 134, 2012. View at Google Scholar
  28. C. Schretter and M. C. Milinkovitch, “OligoFaktory: a visual tool for interactive oligonucleotide design,” Bioinformatics, vol. 22, no. 1, pp. 115–116, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. A. M. Pessoa, S. Pereira, and J. Teixeira, “PrimerIdent: a web based tool for conserved primer design,” Bioinformation, vol. 5, pp. 52–54, 2010. View at Google Scholar
  30. R. Giegerich, F. Meyer, and C. Schleiermacher, “GeneFisher—software support for the detection of postulated genes,” Proceedings of International Conference on Intelligent Systems for Molecular Biology, vol. 4, pp. 68–77, 1996. View at Google Scholar · View at Scopus
  31. R. Kalendar, D. Lee, and A. H. Schulman, “FastPCR software for PCR primer and probe design and repeat search,” Genes, Genomes and Genomics, vol. 3, pp. 1–14, 2009. View at Google Scholar
  32. O. J. Jabado, G. Palacios, V. Kapoor et al., “Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments,” Nucleic Acids Research, vol. 34, no. 22, pp. 6605–6611, 2006. View at Publisher · View at Google Scholar · View at Scopus
  33. D. Rosenkranz, “EasyPAC: a tool for fast prediction, testing and reference mapping of degenerate PCR primers from Alignments or consensus sequences,” Evolutionary Bioinformatics Online, vol. 8, article 151, 2012. View at Google Scholar
  34. B. Dwivedi, R. Schmieder, D. B. Goldsmith, R. A. Edwards, and M. Breitbart, “PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity,” BMC Bioinformatics, vol. 13, article 37, 2012. View at Google Scholar
  35. J. D. Gans, J. Dunbar, S. A. Eichorst, L. V. Gallegos-Graves, M. Wolinsky, and C. R. Kuske, “A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil,” Nucleic Acids Research, vol. 40, no. 12, article e96, 2012. View at Google Scholar
  36. W. A. Kibbe, “OligoCalc: an online oligonucleotide properties calculator,” Nucleic Acids Research, vol. 35, pp. W43–W46, 2007. View at Publisher · View at Google Scholar · View at Scopus