Frameshift detection in prokaryotic genomic sequences

  • Authors:

  • Andrey Kislyuk;Alexandre Lomsadze;Alla L. Lapidus;Mark Borodovsky

  • Affiliations:

  • School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.;Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.;Joint Genome Institute, US Department of Energy (/DOE-/JGI)/, Walnut Creek, California 94598, USA.;Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA/ Division of Computational Science and Engineering, Georg ...

  • Venue:
  • International Journal of Bioinformatics Research and Applications
  • Year:
  • 2009

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Abstract

We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can serve as a useful tool for sequencing quality control in the next generation sequencing. We evaluated the method's accuracy on test sets of annotated genomic sequences with artificial frameshifts in protein coding regions. These tests have shown that the new method performs comparably to the earlier developed FrameD. On the sets of sequences produced by 454 pyrosequencing with sequence errors recovered by Sanger re-sequencing the accuracy of the method was shown to hold at the same level.