DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering

Bioinformatic tools and guideline for PCR primer design

“…Companies engaged in biosoftware development include: Alkami Biosystems, Molecular Biology Insights, PREMIER Biosoft International, IntelliGenetics Inc., Hitachi Inc., DNA Star, Advanced American Biotechnology and Imaging. Some scientists have also developed algorithms and computer programs for various purposes of primer design (Rychlik and Rhoades, 1989;Lowe et al, 1990;Lucas et al, 1991; O'Hara and Venezia, 1991; Tamura et Makarova et al, 1992;Osborne, 1992;Li et al,1997;Plasterer, 1997;Sze et al, 1998;Gorelenkov et al, 2001). Many programs aiding in the design of primers exist (Table 3).…”

Optimal encoding rules for synthetic genes: the need for a community effort

“…To this end, a wealth of software has been developed to help bench scientists achieve reverse translation (Arentzen and Ripka, 1984; Mount and Conrad, 1984; Danckaert et al , 1987; Pesole et al , 1988; Presnell and Benner, 1988; Weiner and Scheraga, 1989; Bains, 1990; Tamura et al , 1991; Libertini and Di Donato, 1992; Makarova et al , 1992; Nash, 1993; Raghava and Sahni, 1994; Withers‐Martinez et al , 1999; Hoover and Lubkowski, 2002; Fuglsang, 2003; Gao et al , 2004; Grote et al , 2005; Jayaraj et al , 2005; Richardson et al , 2006; Villalobos et al , 2006; Wu et al , 2006b; Puigbo et al , 2007). Broadly speaking, this software can be divided into two categories according to algorithmic purpose: one seeking gene designs that facilitate empirical sequence manipulations, the other seeking designs that translate well into protein products.…”

“…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.…”