JCat: A novel tool to adapt codon usage of a target gene to its potential expression host.


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Bioinformatic tools from our team:

JCat was published in NAR (Nucleic Acids Research).

Literature

Grote A, Hiller K, Scheer M, Munch R, Nortemann B, Hempel DC, Jahn D.

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W526-31.

Sharp PM, Li WH

Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons.

Nucleic Acids Res. 1986 Oct 10;14(19):7737-49.

Sharp PM, Li WH

The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications.

Nucleic Acids Res. 1987 Feb 11;15(3):1281-95.

Carafa YA, Brody E, Thermes C

Prediction of Rho-independent Escherichia coli Transcription Terminators - A Statistical Analysis of their RNA Stem-Loop Structures.

J.Mol.Biol. 1990; 216:835-58.

Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL

Prediction of transcription terminators in bacterial genomes.

J Mol Biol. 2000 Aug 4;301(1):27-33.

Zeeberg B

Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes.

Genome Res. 2002 Jun;12(6):944-55.

Roberts RJ, Vincze T, Posfai J, Macelis D

REBASE: restriction enzymes and methyltransferases.

Nucleic Acids Res. 2003 Jan 1;31(1):418-20.

Carbone A, Zinoveyv A, Kepes F

Codon adaptation index as a measure of dominating codon bias

Bioinformatics. 2003 Nov 1;19(16):2005-15.

Friberg M, von Rohr P, Gonnet G

Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression in Saccharomyces cerevisiae.

Yeast. 2004 Oct 15;21(13):1083-93.