Publication Date:
2014-04-11
Description:
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. Availability: Source code is available for download at https://sourceforge.net/projects/dtailor/ Contact: aparkin@lbl.gov or cambray.guillaume@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online (D-Tailor Tutorial).
Print ISSN:
1367-4803
Electronic ISSN:
1460-2059
Topics:
Biology
,
Computer Science
,
Medicine
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