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Bioinformatic tools from our team:

PRODORIC - Prokaryotic Database of Gene Regulation and Regulatory Networks
JVirGel - Virtual 2D-protein gels
PrediSi - PREDIction of SIgnal peptides

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.
PMID: 15980527

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.
PMID: 3534792

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.
PMID: 3547335

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.
PMID: 1702475

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.
PMID: 10926490

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.
PMID: 12045147

Roberts RJ, Vincze T, Posfai J, Macelis D
REBASE: restriction enzymes and methyltransferases.
Nucleic Acids Res. 2003 Jan 1;31(1):418-20.
PMID: 12520038

Carbone A, Zinoveyv A, Kepes F
Codon adaptation index as a measure of dominating codon bias
Bioinformatics. 2003 Nov 1;19(16):2005-15.
PMID: 14594704

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.
PMID: 15484285

 
     

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   © 2004-2008 by Andreas Grote •  andreas.grote@tu-bs.de