Sensitive, Specific Polymorphism Discovery in Bacteria Using Massively Parallel Sequencing

Nat Methods. 2009 Jan;6(1):67-9. doi: 10.1038/nmeth.1286. Epub 2008 Dec 14.


Our variant ascertainment algorithm, VAAL, uses massively parallel DNA sequence data to identify differences between bacterial genomes with high sensitivity and specificity. VAAL detected approximately 98% of differences (including large insertion-deletions) between pairs of strains from three species while calling no false positives. VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic's site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives.

MeSH terms

  • Algorithms
  • Base Sequence
  • DNA, Bacterial / analysis*
  • DNA, Bacterial / genetics*
  • Databases, Nucleic Acid
  • Polymorphism, Genetic / genetics*
  • Sensitivity and Specificity


  • DNA, Bacterial