Optimizing SNP microarray probe design for high accuracy microbial genotyping.

@article{Gardner2013OptimizingSM,
  title={Optimizing SNP microarray probe design for high accuracy microbial genotyping.},
  author={Shea N. Gardner and James B. Thissen and Kevin McLoughlin and Tom Slezak and Crystal J. Jaing},
  journal={Journal of microbiological methods},
  year={2013},
  volume={94 3},
  pages={303-10}
}
Microarrays to characterize single nucleotide polymorphisms (SNPs) provide a cost-effective and rapid method (under 24h) to genotype microbes as an alternative to sequencing. We developed a pipeline for SNP discovery and microarray design that scales to 100's of microbial genomes. Here we tested various SNP probe design strategies against 8 sequenced isolates of Bacillus anthracis to compare sequence and microarray data. The best strategy allowed probe length to vary within 32-40 bp to equalize… CONTINUE READING

References

Publications referenced by this paper.
Showing 1-10 of 22 references

Scalable SNP analyses of 100+ bacterial or viral genomes

S. Gardner, T. Slezak
J. Forensic Res • 2010
View 5 Excerpts
Highly Influenced

Versatile and open software for comparing large genomes

Genome Biology • 2003
View 3 Excerpts
Highly Influenced

Chapter 16 - Forensic Analysis in Bacterial Pathogens

R. T. Okinaka, K. H. Hill, +5 authors P. S. Keim
2011
View 2 Excerpts

Microarrays for Pathogen Detection and Analysis

Briefings in functional genomics • 2011
View 2 Excerpts

Similar Papers

Loading similar papers…