Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (427K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (74)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Ashelford, K. E.
Right arrow Articles by Fry, J. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ashelford, K. E.
Right arrow Articles by Fry, J. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 15 3481-3489
© 2002 Oxford University Press

PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database

Kevin E. Ashelford*, Andrew J. Weightman and John C. Fry

Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK

*To whom correspondence should be addressed. Tel: +44 29 2087 6002; Fax: +44 29 2087 4305; Email: ashelford{at}cardiff.ac.uk

We describe PRIMROSE, a computer program for identifying 16S rRNA probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria. PRIMROSE is designed to use data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides. PRIMROSE includes features to allow user-defined sequence databases to be used. An in silico trial of the program using the RDP database identified oligonucleotides that described their target taxa with a degree of accuracy far greater than that of equivalent currently used oligonucleotides. We identify oligonucleotides for subdivisions of the Proteobacteria and for the Cytophaga–Flexibacter–Bacteroides (CFB) division. These oligonucleotides describe up to 94.7% of their target taxon with fewer than 50 non-target hits, and the authors recommend that they be investigated further. A comparison with PROBE DESIGN within the ARB software package shows that PRIMROSE is capable of identifying oligonucleotides with a higher specificity. PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Severgnini, P. Cremonesi, C. Consolandi, G. Caredda, G. De Bellis, and B. Castiglioni
ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design
Nucleic Acids Res., June 16, 2009; (2009) gkp499v1.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. E. Morales and W. E. Holben
Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis
Appl. Envir. Microbiol., May 1, 2009; 75(9): 2677 - 2683.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
C. Almeida, N. F. Azevedo, C. Iversen, S. Fanning, C. W. Keevil, and M. J. Vieira
Development and Application of a Novel Peptide Nucleic Acid Probe for the Specific Detection of Cronobacter Genomospecies (Enterobacter sakazakii) in Powdered Infant Formula
Appl. Envir. Microbiol., May 1, 2009; 75(9): 2925 - 2930.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
C. Boeckaert, B. Vlaeminck, V. Fievez, L. Maignien, J. Dijkstra, and N. Boon
Accumulation of trans C18:1 Fatty Acids in the Rumen after Dietary Algal Supplementation Is Associated with Changes in the Butyrivibrio Community
Appl. Envir. Microbiol., November 15, 2008; 74(22): 6923 - 6930.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
K. Klitgaard, M. Boye, N. Capion, and T. K. Jensen
Evidence of Multiple Treponema Phylotypes Involved in Bovine Digital Dermatitis as Shown by 16S rRNA Gene Analysis and Fluorescence In Situ Hybridization
J. Clin. Microbiol., September 1, 2008; 46(9): 3012 - 3020.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
G. M. Pumphrey and E. L. Madsen
Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil
Appl. Envir. Microbiol., July 1, 2008; 74(13): 4111 - 4118.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. Sagova-Mareckova, L. Cermak, J. Novotna, K. Plhackova, J. Forstova, and J. Kopecky
Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics
Appl. Envir. Microbiol., May 1, 2008; 74(9): 2902 - 2907.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. Zozaya-Hinchliffe, D. H. Martin, and M. J. Ferris
Prevalence and Abundance of Uncultivated Megasphaera-Like Bacteria in the Human Vaginal Environment
Appl. Envir. Microbiol., March 1, 2008; 74(5): 1656 - 1659.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Militon, S. Rimour, M. Missaoui, C. Biderre, V. Barra, D. Hill, A. Mone, G. Gagne, H. Meier, E. Peyretaillade, et al.
PhylArray: phylogenetic probe design algorithm for microarray
Bioinformatics, October 1, 2007; 23(19): 2550 - 2557.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
N. Guimaraes, N. F. Azevedo, C. Figueiredo, C. W. Keevil, and M. J. Vieira
Development and Application of a Novel Peptide Nucleic Acid Probe for the Specific Detection of Helicobacter pylori in Gastric Biopsy Specimens
J. Clin. Microbiol., September 1, 2007; 45(9): 3089 - 3094.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Feng and E. R.M. Tillier
A fast and flexible approach to oligonucleotide probe design for genomes and gene families
Bioinformatics, May 15, 2007; 23(10): 1195 - 1202.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
M. J. Ferris, J. Norori, M. Zozaya-Hinchliffe, and D. H. Martin
Cultivation-Independent Analysis of Changes in Bacterial Vaginosis Flora Following Metronidazole Treatment
J. Clin. Microbiol., March 1, 2007; 45(3): 1016 - 1018.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB.
Appl. Envir. Microbiol., July 1, 2006; 72(7): 5069 - 5072.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
G. R. Noel and N. Atibalentja
'Candidatus Paenicardinium endonii', an endosymbiont of the plant-parasitic nematode Heterodera glycines (Nemata: Tylenchida), affiliated to the phylum Bacteroidetes.
Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1697 - 1702.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
T. E. Freitag, L. Chang, C. D. Clegg, and J. I. Prosser
Influence of Inorganic Nitrogen Management Regime on the Diversity of Nitrite-Oxidizing Bacteria in Agricultural Grassland Soils
Appl. Envir. Microbiol., December 1, 2005; 71(12): 8323 - 8334.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
A. K. Rowan, R. J. Davenport, J. R. Snape, D. Fearnside, M. R. Barer, T. P. Curtis, and I. M. Head
Development of a Rapid Assay for Determining the Relative Abundance of Bacteria
Appl. Envir. Microbiol., December 1, 2005; 71(12): 8481 - 8490.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W.-H. Chung, S.-K. Rhee, X.-F. Wan, J.-W. Bae, Z.-X. Quan, and Y.-H. Park
Design of long oligonucleotide probes for functional gene detection in a microbial community
Bioinformatics, November 15, 2005; 21(22): 4092 - 4100.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. Kato, S. Haruta, Z. J. Cui, M. Ishii, and Y. Igarashi
Stable Coexistence of Five Bacterial Strains as a Cellulose-Degrading Community
Appl. Envir. Microbiol., November 1, 2005; 71(11): 7099 - 7106.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
F. Warnecke, R. Sommaruga, R. Sekar, J. S. Hofer, and J. Pernthaler
Abundances, Identity, and Growth State of Actinobacteria in Mountain Lakes of Different UV Transparency
Appl. Envir. Microbiol., September 1, 2005; 71(9): 5551 - 5559.
[Abstract] [Full Text] [PDF]

Home page
 J Med MicrobiolHome page
L. McAuliffe, R. J Ellis, J. R Lawes, R. D Ayling, and R. A. Nicholas
16S rDNA PCR and denaturing gradient gel electrophoresis; a single generic test for detecting and differentiating Mycoplasma species
J. Med. Microbiol., August 1, 2005; 54(8): 731 - 739.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
M. J. Ferris, A. Masztal, and D. H. Martin
Use of Species-Directed 16S rRNA Gene PCR Primers for Detection of Atopobium vaginae in Patients with Bacterial Vaginosis
J. Clin. Microbiol., December 1, 2004; 42(12): 5892 - 5894.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
G. Webster, R. J. Parkes, J. C. Fry, and A. J. Weightman
Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments
Appl. Envir. Microbiol., September 1, 2004; 70(9): 5708 - 5713.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
K. Nakamura, S. Haruta, H. L. Nguyen, M. Ishii, and Y. Igarashi
Enzyme Production-Based Approach for Determining the Functions of Microorganisms within a Community
Appl. Envir. Microbiol., June 1, 2004; 70(6): 3329 - 3337.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.