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Table 2 Software and Website Applications for Designing Synthetic Genes.

From: Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

Name Database Codon Engineering Sequence Engineering Oligo-nucleotide Engineering Construct/Vector Engineering Protein Engineering
Gene Composer • CUT • CWeighted Random • Restriction Sites • Gene Synthesis Yes Yes
  • Genes • G:C Content • mRNA structure • Mutagenesis   
  • Constructs • Custom • Repeat Removal    
  • Alignments   • Ambush Stop Codon    
    • User defined Sequences    
Optimizer • CUT • One Amino Acid – one Codon No No No No
   • Guided Random     
   • Custom     
Gene Designer No • One Amino Acid – One Codon • Restriction Sites No No No
   • Random • Repeat Removal    
Gene Optimizer No • Multiple parameter • mRNA structure No No No
    • Repeat Removal    
    • mRNA Splice Sites    
DNA Works No • Random • Restriction Sites • Gene Synthesis No No
  1. Database refers to the presence or absence of a database to store codon usage tables (CUT), gene sequences (Genes), complete plasmid construct sequences (Constructs), and alignments of protein sequences (Alignments). Codon Engineering refers to the methods used for back-translation of amino acid sequences into nucleic acid sequences. Sequence Engineering refers to the ability to alter the nucleic acid sequence to introduce or remove restriction sites, remove sequence repeats, alter potential mRNA secondary structures, remove mRNA splice sites or any other user defined sequence. Oligonucleotide Engineering refers to the ability to design oligonucleotides to for gene synthesis or to create mutagenic primers. Construct/Vector Engineering refers to the ability to visualize and create complete plasmid expression vectors using designed gene sequences. Protein Engineering refers to the ability to create protein alignments to design specific protein constructs. Gene Composer: Emerald Biosystems, http://www.genecomposer.net; Optimizer: Universitat Rovira i Virgili, genomes.urv.es/OPTIMIZER/; Gene Designer: DNA2.0, http://www.dna20.com; Gene Optimizer: GeneArt, http://www.geneart.com; DNA Works: Helix Systems, http://helixweb.nih.gov/dnaworks/.