All codes have been revised for efficiency, consistency and compatibility. In addition, all modules that output gene sequences now offer FASTA output.
The Reverse Translate module takes a protein sequence and replaces each residue with a user-determined codon. Typically, users select one of GeneDesign's codon sets, but they may also define their own. This module now offers Bacillus subtilis and Drosophila melanogaster RSCU data sets. It will now accept a set of protein sequences in the FASTA format. This module is now available as a command line script, where it offers the ability to design sequences reverse translated for more than one organism at a time.
The Codon Juggling module takes a protein coding nucleotide sequence and offers several synonymous, algorithmic variations on it. This module now has a new algorithm, ‘least different RSCU’, which seeks to replace as many codons as possible while minimizing disruption of the original average RSCU value for the sequence. This module is now available as a command line script, where it offers the ability to design sequences using multiple algorithms and for more than one organism at a time.
Restriction Site Subtraction
The Restriction Site Subtraction module takes a protein coding nucleotide sequence and allows the user to specify which restriction sites will be removed without modifying the encoded protein sequence. The Subtraction module has been modified to use the ‘least different RSCU’ algorithm when replacing codons in order to minimize the impact of each edit, and to change as few codons as possible in every edit.
Restriction Enzyme Filter
The restriction enzyme database used by GeneDesign has been updated to include a more current set of commercially available enzymes and their prices (15
). The enzyme choosing module has been updated to add overhang palindromy, heat inactivation, star activity, optimal incubation temperature, incubation buffer and methylation sensitivity as filter criteria.