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Bioinformatic tools from our team:

PRODORIC - Prokaryotic Database of Gene Regulation and Regulatory Networks

JCat was published in NAR (Nucleic Acids Research).


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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