Thermodynamic post-processing versusGC-content pre-processing for DNA codessatisfying the hamming distance and reverse-complement constraints

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DOIResolve DOI: http://doi.org/10.1109/TCBB.2014.2299815
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TypeArticle
Journal titleIEEE/ACM Transactions on Computational Biology and Bioinformatics
ISSN1545-5963
Volume11
Issue2
Article number6710171
Pages441452; # of pages: 12
SubjectAlgorithms; 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
AbstractStochastic, 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.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC); Information and Communication Technologies (ICT-TIC)
Peer reviewedYes
NPARC number21272283
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Record identifier08003509-3572-42ca-8174-2df1254282e1
Record created2014-07-23
Record modified2016-05-09
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