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Bioinformatics. 2014 Jan 13. [Epub ahead of print]

D-Tailor: automated analysis and design of DNA sequences.

Author information

  • 1Department of Bioengineering, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA, Computer Science and Technology Center, School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

Abstract

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).

PMID:
24398007
[PubMed - as supplied by publisher]
PMCID:
PMC3982154
Free PMC Article

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