Computational Methods for Strain Design - Synthetic Biology - page 139

TABLE 8.1 Computational Tools in Designing Synthetic Biological Components
Synthetic system Website Refs

DNA assembly
GeneDesigner

https://www.dna20.com/genedesigner2 29

GeneDesign http://www.genedesign.org 28

j5 http://j5.jbei.org 26

Asmparts http://soft.synth-bio.org/asmparts.html 30

Gene Composer http://www.genecomposer.net 27

Biomolecular design
Rosetta

http://www.rosettacommons.org 25

RBSDesigner http://rbs.kaist.ac.kr 21

RBS Calculator https://salis.psu.edu/software 19

Optimizer http://genomes.urv.cat/OPTIMIZER 24

Genetic circuit design
Genetdes

http://soft.synth-bio.org/genetdes.html 31

RoVerGeNe http://iasi.bu.edu/ batt/rovergene/rovergene.htm 7

B

OptCircuit http://maranas.che.psu.edu/research_circuits.htm 32

GEC http://lepton.research.microsoft.com/webgec 16

Biojade http://web.mit.edu/jagoler/www/biojade 36

GenoCAD http://www.genocad.org 33

SynBioSS http://synbioss.sourceforge.net 34

TinkerCell http://www.tinkercell.com 35

Pathway prediction
EnzMatcher stand-alone software 1

KEGG PathPred http://www.genome.jp/tools/pathpred 39

BNICE http://systemsbiology.northwestern.edu/bnice 2

UM-BBD Pathway prediction http://umbbd.msi.umn.edu/predict 38

OptStrain framework (No website) 42

147

DESHARKY http://soft.synth-bio.org/desharky.html 43

RetroPath http://www.issb.genopole.fr/ B faulon/retropath.php 12

FMM http://fmm.mbc.nctu.edu.tw/index.php 40

CarbonSearch http://www.kavrakilab.org/atommetanet 41

Furthermore, it is possible to optimize the codons of open reading frames for protein
expression for a specific host organism. 29

GeneDesign is a web-based tool that provides modules, algorithms, restriction enzyme
library, and batch processing capabilities. Each module can be in charge of different tasks,
such as reverse translation, codon juggling, and building block design. 28 For example, after a
target protein has been characterized and its presence inside a novel gene circuit has been
confirmed, the protein can be reverse translated back to DNA, whose sequence is then
modified and engineered to optimally function in the host organism which the gene circuit
is to be incorporated into.

Another tool that can automate the design of DNA assembly protocol is j5, a web-based
software tool. 26 The design process of j5 includes the optimization of costs, design
specification rule enforcement, strategies in hierarchical assembly to minimize assembly
errors, and the manual or automated construction of scarless combinatorial DNA libraries.
The design algorithms are generally compatible with other DNA construction
methodologies, and can be used to complement other DNA assembly tools ( Table 8.1 ).

Genetic Circuit Design
A number of computational methods have already been developed to facilitate system
design. To date these methods have concentrated mainly on the design of small