|
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
|
- 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/.
