title: D-Tailor: automated analysis and design of DNA sequences.
abstract: 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.
  
  
  
  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.
  
  
  
  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).
authors.affiliation: Department 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 Department 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 Department 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.
authors.forename: Joao C
authors.initials: JC
authors.lastname: Guimaraes
authors.affiliation: Department 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.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rocha
authors.affiliation: Department 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 Department 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 Department 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.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.affiliation: Department 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.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Cambray
mesh_terms: D019295:Computational Biology; D004247:DNA; D004926:Escherichia coli / Q000235:genetics; D009010:Monte Carlo Method; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA