Design-A-Gene with GeneDesign.

The manual design of synthetic genes is a tedious and error-prone process-even for very short genes-and it becomes completely infeasible when multiple synthetic genes are needed. GeneDesign is a set of modules that automate batch nucleotide manipulation. Here, we explain the installation, configuration, and use of GeneDesign as part of a synthetic design workflow.

[1]  D C Shields,et al.  Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. , 1988, Nucleic acids research.

[2]  Scott Chacon,et al.  Pro Git , 2009, Apress.

[3]  J. Boeke,et al.  GeneDesign: rapid, automated design of multikilobase synthetic genes. , 2006, Genome research.

[4]  Paul M. Sharp,et al.  Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes , 1986, Nucleic Acids Res..

[5]  Jef D Boeke,et al.  Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course , 2009, Genetics.

[6]  N. Sugimoto,et al.  Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. , 1996, Nucleic acids research.

[7]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[8]  D. G. Gibson,et al.  Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides , 2009, Nucleic acids research.

[9]  Paul M. Sharp,et al.  Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases , 1994, Nucleic Acids Res..

[10]  Romualdas Vaisvila,et al.  USER™ friendly DNA engineering and cloning method by uracil excision , 2007, Nucleic acids research.

[11]  R E Rhoads,et al.  Optimization of the annealing temperature for DNA amplification in vitro. , 1990, Nucleic acids research.