Approximate All-Pairs Suffix/Prefix Overlaps

  • Niko Välimäki
  • Susana Ladra
  • Veli Mäkinen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6129)


Finding approximate overlaps is the first phase of many sequence assembly methods. Given a set of r strings of total length n and an error-rate ε, the goal is to find, for all-pairs of strings, their suffix/prefix matches (overlaps) that are within edit distance k = ⌈εℓ⌉, where ℓ is the length of the overlap. We propose new solutions for this problem based on backward backtracking (Lam et al. 2008) and suffix filters (Kärkkäinen and Na, 2008). Techniques use nH k  + o(nlogσ) + rlogr bits of space, where H k is the k-th order entropy and σ the alphabet size. In practice, methods are easy to parallelize and scale up to millions of DNA reads.


Edit Distance Short Read Approximate String Match Dynamic Programming Table Short Read Mapping 
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 2010

Authors and Affiliations

  • Niko Välimäki
    • 1
  • Susana Ladra
    • 2
  • Veli Mäkinen
    • 1
  1. 1.Department of Computer ScienceUniversity of HelsinkiFinland
  2. 2.Department of Computer ScienceUniversity of A CoruñaSpain

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