FluDen Primer DB-PCR Primer Database for Influenza A and Dengue Virus

Authors

  • Raghavendra Krishnappa Department of Microbiology, Karpagam University
  • Rajendran Paramasivam Sri Ramachandra Medical College & Research Institute, Sri Ramachandra University

DOI:

https://doi.org/10.6000/1927-3037.2015.04.03.2

Keywords:

PCR, Influenza, Dengue, NetPrimer, FastPCR

Abstract

FluDen Primer Database (http://www.fludenpdb.com) has been designed and developed as a web application program to provide free access to the in-silico designed multiple potential primers for PCR detection and quantification assays for Influenza and dengue viruses. This program also permits user to submit sequence of their choice for primer design. The database contains primer records for Influenza and dengue viruses which cause infection in Humans. As of 2014 there are 142 primer sets for screening 32 genes/regions of Influenza and dengue viruses together. Application contain gene information, assay details such as oligonucleotide sequence, primer properties and reaction conditions, publication information. We have developed a resource, FluDen Primer DB which contains primer that can be used for PCR under provided amplification conditions for each primer pair. A distinguish feature of the FlueDen is the primers listed in DB are the products of PCR design application which are experimentally validated. Primers for the FluDen were designed using current genomic information available from the National Center for Biotechnology Information (NCBI).

References


[1] Yanga S, Rothmana RE. PCR-based diagnostics for infectious diseases: uses, limitations and future applications in acute-care settings. Lancet Infect Dis 2004; 4(6): 337-48. http://dx.doi.org/10.1016/S1473-3099(04)01044-8
[2] Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25(17): 3389-402. http://dx.doi.org/10.1093/nar/25.17.3389
[3] Kalendar R, Lee D, Schulman AH. Java web tools for PCR, in silico PCR and oligonucleotide assembly and analysis. Genomics 2011; 98(2): 137-144. http://dx.doi.org/10.1016/j.ygeno.2011.04.009
[4] Kalendar R, Lee D, Schulman AH. FastPCR software for PCR, in silico PCR and oligonucleotide assembly andanalysis. DNA Cloning and Assembly Methods. Methods in Mol Biol. (Clifton NJ Ed.) 2014, 1116: 271-302. ISBN 978-1-62703-763-1. http://dx.doi.org/10.1007/978-1-62703-764-8_18
[5] Zhang X, Ding L. Selection of reference genes for gene expression studies in human neutrophils by real-time PCR. BMC Mol Biol 2005; 6: 4. http://dx.doi.org/10.1186/1471-2199-6-4
[6] Verhelst R, Verstraelen H, Claeys G, et al. Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis” BMC Microbiol 2004; 4: 16. http://dx.doi.org/10.1186/1471-2180-4-16
[7] Hayden MJ, Sharp PJ. Targeted development of informative microsatellite (SSR) markers. Nucleic Acids Res 2001; 29(8): e44. http://dx.doi.org/10.1093/nar/29.8.e44
[8] Krishnappa R, Paramasivam R. Primers for dengue virus strains based on their sequence variability. Open Access Library J 2015; 2: 1-6. http://dx.doi.org/10.4236/oalib.1101104
[9] Ranjit S, Kissoon N. Dengue hemorrhagic fever and shock syndromes. Pediatr Crit Care Med 2011; 12: 90-100. http://dx.doi.org/10.1097/PCC.0b013e3181e911a7
[10] Whitehorn J, Farrar J. Dengue. Brit Med Bull 2010; 95: 161-73. http://dx.doi.org/10.1093/bmb/ldq019
[11] Varatharaj A. Encephalitis in the clinical spectrum of dengue infection. Neurol India 2010; 58: 585-91. http://dx.doi.org/10.4103/0028-3886.68655
[12] Knoop KJ, Stack LB, Storrow A, Thurman RJ. Tropical Medicine. Atlas of Emergency Medicine. 3rd. Edition, McGraw-Hill Professional, New York, 2010; pp. 658-9. ISBN 0-07-149618-1.
[13] Peeling RW, Artsob H, Pelegrino JL, et al. WHO, on behalf of TDR (WHO/TDR) Nature Rev Microbiol 2010, S30-S37. http://dx.doi.org/10.1038/nrmicro2459
[14] Arias CF, Escalera-Zamudio M, de los Dolores Soto-Del Río M, et al. Molecular Anatomy of 2009 Influenza Virus A (H1N1). Arch Med Res 2009; 40: 643-54. http://dx.doi.org/10.1016/j.arcmed.2009.10.007
[15] Taubenberger JK, Reid AH, Janczewski TA, et al. Integrating historical, clinical and molecular genetic data in order to explain the origin and virulence of the 1918 Spanish influenza virus. Philos Trans R Soc Lond B Biol Sci 2001; 356: 1829-39. http://dx.doi.org/10.1098/rstb.2001.1020
[16] Basler CF, Aguilar PV. Progress in identifying virulence determinants of the 1918 H1N1 and the Southeast Asian H5N1 influenza A viruses. Antiviral Res 2008; 79: 166-78. http://dx.doi.org/10.1016/j.antiviral.2008.04.006
[17] George KS. Diagnosis of influenza virus. Methods Mol Biol 2012; 865: 53-69. http://dx.doi.org/10.1007/978-1-61779-621-0_4

Downloads

Published

2015-12-01

Issue

Section

Articles