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Fast and Accurate Genome Anchoring Using Fuzzy Hash Maps

  • John Healy
  • Desmond Chambers
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)

Abstract

Although hash-based approaches to sequence alignment and genome assembly are long established, their utility is predicated on the rapid identification of exact k-mers from a hash-map or similar data structure. We describe how a fuzzy hash-map can be applied to quickly and accurately align a prokaryotic genome to the reference genome of a related species. Using this technique, a draft genome of Mycoplasma genitalium, sampled at 1X coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The fuzzy approach to alignment, ordered and orientated more than 65% of the reads from the draft genome in under 10 seconds, with an error rate of <1.5%. Without sacrificing execution speed, fuzzy hash-maps also provide a mechanism for error tolerance and variability in k-mer centric sequence alignment and assembly applications.

Keywords

Draft Genome Edit Distance Hash Code Mycoplasma Genitalium Fuzzy Index 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • John Healy
    • 1
  • Desmond Chambers
    • 2
  1. 1.Department Computing & MathematicsGalway-Mayo Institute of TechnologyIreland
  2. 2.Department of Information TechnologyNational University of IrelandGalwayIreland

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