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:
-;-;-;-;-;-;-
Venue:
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Year:
2002

Citing 3
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Abstract

We present an efficient algorithm for determining whether all molecules in a combinatorial set of DNA or RNA strands are structure free, and thus available for bonding to their Watson-Crick complements. This work is motivated by the goal of testing whether strands used in DNA computations or as molecular bar-codes are structure free, where the strands are concatenations of short words. We also present an algorithm for determining whether all words in S*, for some finite set S of equi-length words, are structure-free.