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Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.

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.

Pubmed ID: 19079253


  • Nusbaum C
  • Ohsumi TK
  • Gomez J
  • Aquadro J
  • Victor TC
  • Warren RM
  • Hung DT
  • Birren BW
  • Lander ES
  • Jaffe DB


Nature methods

Publication Data

January 31, 2009

Associated Grants

  • Agency: NHGRI NIH HHS, Id: R01 HG003474
  • Agency: NHGRI NIH HHS, Id: R01 HG003474-01A1
  • Agency: NHGRI NIH HHS, Id: R01 HG003474-02
  • Agency: NHGRI NIH HHS, Id: R01 HG003474-03
  • Agency: NHGRI NIH HHS, Id: R01 HG003474-04

Mesh Terms

  • Algorithms
  • Base Sequence
  • DNA, Bacterial
  • Databases, Nucleic Acid
  • Polymorphism, Genetic
  • Sensitivity and Specificity