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Algorithms for testing that sets of DNA words concatenate without secondary structure

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Abstract

We present an efficient algorithm for determining whether all moleculesin a combinatorial set of DNA or RNA strandsare structure free, and thus availablefor bonding to their Watson-Crick complements.This work is motivated by the goalof testing whether strands used in DNAcomputations or as molecular bar-codesare structure free, where the strands areconcatenations of short words. We alsopresent an algorithm for determining whetherall words in S*, for some finite setS of equi-length words, are structure free.

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Authors and Affiliations

  1. The Department of Computer Science, University of British Columbia, ???

    Mirela Andronescu

  2. Georgia Institute of Technology, College of Computing, ???

    Danielle Dees

  3. Computer Science Department, Rose-Hulman Institute of Technology, ???

    Laura Slaybaugh

  4. The Department of Computer Science, University of British Columbia, ???

    Yinglei Zhao & Anne Condon

  5. Computer Science Department, State University of New York at Stony Brook, USA

    Barry Cohen & Steven Skiena

Authors
  1. Mirela Andronescu
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  2. Danielle Dees
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  3. Laura Slaybaugh
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  4. Yinglei Zhao
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  5. Anne Condon
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  6. Barry Cohen
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  7. Steven Skiena
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Correspondence to Anne Condon.

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Andronescu, M., Dees, D., Slaybaugh, L. et al. Algorithms for testing that sets of DNA words concatenate without secondary structure. Natural Computing 2, 391–415 (2003). https://doi.org/10.1023/B:NACO.0000006770.91995.ec

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  • DOI: https://doi.org/10.1023/B:NACO.0000006770.91995.ec

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