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Table 1 Public codon optimization softwares.

From: Gene Designer: a synthetic biology tool for constructing artificial DNA segments

Name Features Comment Reference
  RE Macintosh [49]
GMAP RE   [50]
CalcGene CUT   [51]
COD OP CUT, RE, DO Unix perl [52]
DNA Works CUT, RE, DO Web browser [53]
Codon Optimizer CUT, RE   [54]
Prot2DNA CUT, RE, mSeq, Rep Precursor to Gene Designer [4]
Gene2Oligo DO Web browser [55]
UpGene CUT, DO   [56]
GeMS CUT, RE, mSeq, DO Web browser [57]
JCat CUT, RE Web browser [58]
Synthetic Gene Designer CUT, RE, DO Web browser [59]
  1. Software with features similar to the codon optimization module of Gene Designer. CUT indicates that one or more codon usage tables are referenced during reverse translation of the protein sequence. RE indicates that restriction endonuclease sites can be identified and silently removed and/or inserted. Rep indicates that repeats and/or inverted repeats can be silently removed. mSeq indicates that mRNA secondary structures can be silently removed. DO identifies software that includes a module for the design of oligonucleotides for gene synthesis