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Open Access Highly Accessed Methodology article

BactQuant: An enhanced broad-coverage bacterial quantitative real-time PCR assay

Cindy M Liu12, Maliha Aziz1, Sergey Kachur15, Po-Ren Hsueh3, Yu-Tsung Huang4, Paul Keim12 and Lance B Price1*

Author Affiliations

1 Division of Pathogen Genomics, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86001, USA

2 Center for Microbial Genetics and Genomics, Applied Research & Development Building,, Northern Arizona University, 1298 S. Knoles Drive, Flagstaff, AZ, 86011, USA

3 Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, No. 7, Chung-Shan South Road, Taipei, Taiwan

4 Department of Internal Medicine, Far Eastern Memorial Hospital, No.21, Nanya S. Rd., New Taipei City, Taiwan

5 Current Address: Ross University School of Medicine, 630 US Highway 1, North Brunswick, NJ, 08902, USA

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BMC Microbiology 2012, 12:56  doi:10.1186/1471-2180-12-56

Published: 17 April 2012

Additional files

Additional file 1 :

Figure S1. Figure S1 containing the in silico coverage analysis using the relaxed criteria.

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Additional file 2 :

Figure S2A-E. Standard curve amplification plots using mixed templates.

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Additional file 3 :

Figure S3A-E. Amplification plots of the non-perfect match targets, including C. trachomatis, C. pneumoniae, C. gilvus, B. burgdorferi, and E. vulneris.

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Additional file 4 :

Figure S4A-E. Coefficient of variance (CoV) distribution across assay dynamic range for mixed templates.

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Additional file 5 :

Supplemental File 1. Detailed results for BactQuant using the stringent criteria.

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Additional file 6 :

Supplemental File 2. Detailed results for BactQuant using the relaxed criteria.

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Additional file 7 :

Supplemental File 3. Detailed results for published assay using the stringent criteria.

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Additional file 8 :

Supplemental File 4. Detailed results from published assay using the relaxed criteria.

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Additional file 9 :

Table S1. Base distribution output used in primer and probe design, with the bolded base signifying the selected base(s) and incorporation of more than one allele at a given nucleotide position was accomplished using degenerate bases. The alignment position information in the base distribution file contains many gaps as a result from the sequence alignment and differs from the E. coli region information from Table 1.

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