Pairwise alignment with scoring on tuples

  • Lukas Knecht
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 937)


Pairwise alignment of two sequences a, b usually assumes a and b being sequences over the same alphabet A and a scoring function s: A×A→ℝ operating on symbol pairs. The framework presented here extends this to a scoring function s: A p ×B q →ℝ operating on p-tuples and q-tuples of symbols, where the scoring tuples can have an arbitrary (but not complete) overlap.

We show that, if the alphabets A and B are finite and p and q are constant, the resulting algorithms have the same asymptotic time and space complexity as their single symbol counterparts.

This framework has been applied successfully to the codon-wise alignment of prokaryotic and eukaryotic genes.


Space Complexity Dynamic Programming Algorithm Pairwise Alignment Good Alignment Global Alignment 
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 1995

Authors and Affiliations

  • Lukas Knecht
    • 1
  1. 1.Institute for Scientific ComputingETH ZurichZurichSwitzerland

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