Table 2.

Summary of Computational Tools and Databases for Pathway Optimization Highlighted in This Review

Name	Category	Target	Function	Key Features	URL	Reference
RetroPath 2.0	Computational tool	Biosynthetic genes	Artificial pathway design	Automated open source workflow for retrosynthesis based on generalized reaction rules	https://www.myexperiment.org/workflows/4987.html	(Delepine et al., 2018)
Kyoto Encyclopedia of Genes and Genomes (KEGG)	Database	Biosynthetic Genes		Database for systematic analysis of gene functions, linking genomic information with higher order functional information	https://www.genome.jp/kegg/	(Kanehisa and Goto, 2000)
1000 Plants (1KP) Project	Database	Biosynthetic genes		Transcriptome data from over 1,000 plant species	http://www.bioinfodata.org/app/Blast4OneKP/home/	(Matasci et al., 2014)
CoStar	Computational tool	Biosynthetic genes	Codon optimization	Optimization of gene sequences by avoiding hairpins, GC content variation and repeat	http://life.sysu.edu.cn/COStar/COStar.html	(Liu et al., 2014)
Presyncodon	Computational tool	Biosynthetic genes	Codon optimization	Design of gene sequences for optimized heterologous expression by machine learning	http://www.mobioinfor.cn/presyncodon_www/index.html	(Tian et al., 2018)
BacPP	Computational tool	Promoter	Promoter prediction	Identification of promoters from genome sequences by a machine learning algorithm	www.bacpp.bioinfoucs.com/home	(Silva et al., 2011, Silva et al., 2016)
WebGeSter DB	Database	Terminator		Database containing a million terminators identified in 1,060 bacterial genome sequences and 798 plasmids	http://pallab.serc.iisc.ernet.in/gester	(Mitra et al., 2011)
RBS Calculator	Computational tool	RBS	RBS design	Control of expression level by designing RBSs with various strength	http://www.salis.psu.edu/software	(Salis et al., 2009, Salis, 2011, Borujeni et al., 2014, Farasat et al., 2014)
ClusterCAD	Computational tool	Biosynthetic genes	Protein engineering	Design of chimeric PKSs	https://clustercad.jbei.org/	(Eng et al., 2018)