| DOI | Resolve DOI: https://doi.org/10.1109/TCBB.2014.2299815 |
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| Author | Search for: Tulpan, D.1; Search for: Smith, D.H.; Search for: Montemanni, R. |
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| Affiliation | - National Research Council of Canada. Information and Communication Technologies
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| Format | Text, Article |
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| Subject | Algorithms; Bioinformatics; DNA; Hamming distance; Melting point; Stochastic systems; Construction algorithms; DNA design; Linear codes; Post processing; Pre-processing; reverse-complement; Stochastic local searches; Thermodynamic calculations; Gene encoding |
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| Abstract | Stochastic, meta-heuristic and linear construction algorithms for the design of DNA strands satisfying Hamming distance and reverse-complement constraints often use a GC-content constraint to pre-process the DNA strands. Since GC-content is a poor predictor of DNA strand hybridization strength the strands can be filtered by post-processing using thermodynamic calculations. An alternative approach is considered here, where the algorithms are modified to remove consideration of GC-content and rely on post-processing alone to obtain large sets of DNA strands with satisfactory melting temperatures. The two approaches (pre-processing GC-content and post-processing melting temperatures) are compared and are shown to be complementary when large DNA sets are desired. In particular, the second approach can give significant improvements when linear constructions are used. © 2014 IEEE. |
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| Publication date | 2014 |
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| In | |
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| Language | English |
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| Peer reviewed | Yes |
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| NPARC number | 21272283 |
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| Export citation | Export as RIS |
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| Report a correction | Report a correction (opens in a new tab) |
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| Record identifier | 08003509-3572-42ca-8174-2df1254282e1 |
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| Record created | 2014-07-23 |
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| Record modified | 2020-04-22 |
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