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. 2007 Sep 18;3:134. doi: 10.1038/msb4100176

Figure 2.

Figure 2

The gene design software shown as a network of citations by date of publication. Each of the 37 nodes represents a specific software application for gene design; arrows indicate acknowledgements (citations) of pre-existing, published software. Appropriate web development would alleviate this patchy awareness of competing efforts, and could eliminate inefficient and needless duplication of effort. Abbreviations: BBOCUS: BackTranslation Based On Codon Usage Strategy; BT: BACKTR (Pesole et al, 1988); bt: backtrans (Mount and Conrad, 1984); CO: Codon Optimizer (Fuglsang, 2003); CODOP: CODon OPtimization (Withers-Martinez et al, 1999); DB: DNA Builder (Pacific Northwest National Laboratory); DIROM (Makarova et al, 1992); DW: DNAWorks (Hoover and Lubkowski, 2002); EB: EasyBack (University of Catania, Italy); G.D: Gene.Design (Weiner and Scheraga, 1989) G_D: Gene Designer (Villalobos et al, 2006); G_Dn, GeneDn (Ju et al, 1998); GC: Gene Composer (by Emerald Biosystems); GD: GeneDesign (Richardson et al, 2006); ged: gene design (Presnell and Benner, 1988); GeMS: Gene Morphing System (Jayaraj et al, 2005); GF: The Gene Forge (by AptaGen LLC); GMAP (Raghava and Sahni, 1994); GO: GeneOptimizer (by GeneArt, Germany); IBG: IBG GeneDesigner (Vogelbacher et al, 2006); JCat: Java Codon Adaptation Tool (Grote et al, 2005); LBT: Locally Sensitive BackTranslation; Leto (by Entelechon Inc.) OG: OptGene (by Ocimum Biosolutions); P2D: Protein2DNA (by DNA 2.0 Inc); PGen: PrimerGen (Nash, 1993); PINCERS (Tamura et al, 1991); PO: Primo Optimum (by Chang Bioscience); RESTRI (Libertini and Di Donato, 1992); RT: Reverse Translate (Danckaert et al, 1987); SGD: Synthetic Gene Designer (Wu et al, 2006a, 2006b); SMS: Sequence Manipulation Suite (Stothard, 2000); THOYO (Bains, 1990); TIP: Traducción Inversa de Proteínas/Protein Backtranslation (Moreira and Maass, 2004); U1: unnamed1 (Arentzen and Ripka, 1984); U2: unnamed2 (Danckaert et al, 1987); UpG: UpGene (Gao et al, 2004). Applications shown in dashed lines indicate software that has never appeared in peer reviewed scientific literature.