The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
Open accessAbstract
Background: Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes. Results: Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference. Conclusion: Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.
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Cites
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
Codon bias and heterologous protein expression
Gustafsson, C., Govindarajan, S., & Minshull, J. (2004) · Trends in Biotechnology · doi:10.1016/j.tibtech.2004.04.006 · Cited by 1,330
Self-citationCello, J., Paul, A. V., & Wimmer, E. (2002) · Science · doi:10.1126/science.1072266 · Cited by 980
Benner, S. A., & Sismour, A. M. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1637 · Cited by 834
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
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“The DNA melting temperature calculation is performed using the nearest neighbor method[47,48].”
MethodThe influence of codon context on genetic code translation
Bossi, L., & Roth, J. R. (1980) · Nature · doi:10.1038/286123a0 · Cited by 284
Nonrandom utilization of codon pairs in Escherichia coli.
Gutman, G. A., & Hatfield, G. W. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.10.3699 · Cited by 261 · cited 1×
“Aside from the experimentally validated cases of codon context effect on protein expression levels, there are several publications where in which codon context effects have been proposed based on in silico analysis of genomes [41-43].”
BackgroundComparative context analysis of codon pairs on an ORFeome scale
Moura, G., Pinheiro, M., Silva, R., Miranda, I., Afreixo, V., Dias, G., Freitas, A., Oliveira, J. L., & Santos, M. A. (2005) · Genome Biology · doi:10.1186/gb-2005-6-3-r28 · Cited by 90
Cited by
Refinement of Tools for Targeted Gene Expression in Drosophila
Pfeiffer, B. D., Ngo, T.-T. B., Hibbard, K. L., Murphy, C., Jenett, A., Truman, J. W., & Rubin, G. M. (2010) · Genetics · doi:10.1534/genetics.110.119917 · Cited by 1,153
Advances in COVID-19 mRNA vaccine development
Fang, E., Liu, X., Li, M., Zhang, Z., Song, L., Zhu, B., Wu, X., Liu, J., Zhao, D., & Li, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00950-y · Cited by 601
A critical analysis of codon optimization in human therapeutics
Mauro, V. P., & Chappell, S. A. (2014) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2014.09.003 · Cited by 343
The APC/C maintains the spindle assembly checkpoint by targeting Cdc20 for destruction
Nilsson, J., Yekezare, M., Minshull, J., & Pines, J. (2008) · Nature Cell Biology · doi:10.1038/ncb1799 · Cited by 295
Self-citationOptimization in computational systems biology
Banga, J. R. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-47 · Cited by 278
Metadata
- Authors
- Villalobos, A., Ness, J. E., Gustafsson, C., Minshull, J., & Govindarajan, S.
- Venue
- BMC Bioinformatics
- Published
- 2006-06-06
- Volume
- 7
- Issue
- 1
- Pages
- 285-285
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1760665500
- Cited by
- 376
- References
- 8
- FWCI
- 4.79
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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