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Algorithms for testing that sets of DNA words concatenate without secondary structure |
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| Authors: | Andronescu Mirela Dees Danielle Slaybaugh Laura Zhao Yinglei Condon Anne Cohen Barry Skiena Steven |
| Affiliation: | 1.The Department of Computer Science, University of British Columbia, ??? ;2.Georgia Institute of Technology, College of Computing, ??? ;3.Computer Science Department, Rose-Hulman Institute of Technology, ??? ;4.The Department of Computer Science, University of British Columbia, ??? ;5.Computer Science Department, State University of New York at Stony Brook, USA ; |
| 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. This revised version was published online in June 2006 with corrections to the Cover Date. |
| Keywords: | RNA secondary structure testing DNA word sets |
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