Open Access Software

PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

Jiqiang Yao1, Hong Lin2, Allen Van Deynze3, Harshavardhan Doddapaneni24, Martha Francis5, Eliana Gertrudes Macedo Lemos6 and Edwin L Civerolo2*

Author Affiliations

1 Citrus Research Board, 323 W. Oak Street, Visalia, CA 93291, USA

2 USDA-ARS, San Joaquin Valley Agricultural Science Center, Parlier, CA 93648, USA

3 Seed Biotechnology Center, University of California, One Shields Ave, Davis, CA 95616, USA

4 University of California Davis, Department of Viticulture and Enology, Davis, CA 95616, USA

5 University of California, Department of Plant Pathology, CA 95616, USA

6 Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, s/n, km 5, 14884-900 Jaboticabal, São Paulo, Brasil

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BMC Microbiology 2008, 8:185  doi:10.1186/1471-2180-8-185

Published: 20 October 2008

Additional files

Additional file 1:

The specific primers designed for 9a5c, Temecula1 and Dixon Strains of Xylella fastidiosa. The specific primers designed for strains of Xylella fastidiosa using PrimerSNP.

Format: DOC Size: 263KB Download file

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Open Data

Additional file 2:

The result of experimental validation of the specific primers designed for 9a5c , Temecula1 and Dixon Strains of Xylella fastidiosa. The data provided the experimental validation of the specific primers that are designed using PrimerSNP.

Format: DOC Size: 242KB Download file

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Open Data

Additional file 3:

t-test on the effect of weight score and free energy (ΔG°) on the specificity of primers. The data provided the statistical analysis of the primers' specificity of two groups' primers that have different values of weight score and free energy (ΔG°).

Format: DOC Size: 42KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data