JCat: a novel tool to adapt codon usage of a target gene to its potential expression host
By A. Grote, Karsten Hiller, M. Scheer, R. Münch, B. Nörtemann, D. Hempel, D. Jahn. Nucleic Acids Res., 2005
1,464 citations recorded by the source corpus.
A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at .
Subfields: Molecular Biology
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Citations in the corpus
- CAIcal: A combined set of tools to assess codon usage adaptation (2008, methodology): “A number of programs and servers that calculate CAI for a gene or a group of genes are available elsewhere, such as CodonW, EMBOSS [15], CAIJava [3], CAI Analyser [8], as well as JCAT [16] and the CAI Calculator [5].”
- Gene Designer: a synthetic biology tool for constructing artificial DNA segments (2006, background): “CalcGene CUT [51] COD OP CUT, RE, DO Unix perl [52] DNA Works CUT, RE, DO Web browser [53] Codon Optimizer CUT, RE [54] Prot2DNA CUT, RE, mSeq, Rep Precursor to Gene Designer [4] Gene2Oligo DO Web browser [55] UpGene CUT, DO [56] GeMS CUT, RE, mSeq, DO Web browser [57] JCat CUT, RE Web browser [ 58 ”