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

Authors:
Mirela Andronescu;Danielle Dees;Laura Slaybaugh;Yinglei Zhao;Anne Condon;Barry Cohen;Steven Skiena
Affiliations:
University of British Columbia, The Department of Computer Science;Georgia Institute of Technology, College of Computing;Rose-Hulman Institute of Technology, Computer Science Department;University of British Columbia, The Department of Computer Science;University of British Columbia, The Department of Computer Science (Author for correspendence, e-mail: condon@cs.ubc.ca);State University of New York at Stony Brook, Computer Science Department;State University of New York at Stony Brook, Computer Science Department
Venue:
Natural Computing: an international journal
Year:
2003

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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.