Journal
BIOINFORMATICS
Volume 30, Issue 8, Pages 1087-1094Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt742
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Funding
- National Science Foundation [04-570/0540879]
- Fundacao para a Ciencia e a Tecnologia (FCT) [SFRH/BD/47819/2008]
- Human Frontiers Science Program [LT000873/2011-L]
- Bettencourt Schueller foundation
- European Regional Development Fund (ERDF) through the COMPETE Programme
- FCT [FCOMP-01-0124-FEDER-015079, PEst-OE/EEI/ UI0752/2011]
- Fundação para a Ciência e a Tecnologia [SFRH/BD/47819/2008] Funding Source: FCT
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Motivation: Current advances in DNA synthesis, cloning and sequencing technologies afford high-throughput implementation of artificial sequences into living cells. However, flexible computational tools for multi-objective sequence design are lacking, limiting the potential of these technologies. Results: We developed DNA-Tailor (D-Tailor), a fully extendable software framework, for property-based design of synthetic DNA sequences. D-Tailor permits the seamless integration of multiple sequence analysis tools into a generic Monte Carlo simulation that evolves sequences toward any combination of rationally defined properties. As proof of principle, we show that D-Tailor is capable of designing sequence libraries comprising all possible combinations among three different sequence properties influencing translation efficiency in Escherichia coli. The capacity to design artificial sequences that systematically sample any given parameter space should support the implementation of more rigorous experimental designs.
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