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JCAT (Java Codon Adaptation Tool) 1.0


Description of

JCAT (Java Codon Adaptation Tool)


DNA sequence analysis made easy. The CodonAdaptationTool (JCAT) presents a simple method to adapt the Codon Usage to most sequenced prokaryotic organisms and selected eukaryotic organisms. The codon adaptation plays a major role in cases where foreign genes are expressed in hosts and the codon usage of the host differs from that of the organism where the gene stems from. Unadapted codons in the host can for example lead to a minor expression rate.The adaptation is based on CAI-values proposed by PM Sharp et.al. The CAI-values were calculated by applying an algorithm from A Carbone et. al. The eukaryotic genomes of mouse and human contain different kinds of biases along the chromosomes and the algorithm is not perfectly conformable for this problem. Results in this field should be handled with care. The mean codon usage for a certain organism was derrived by summing over all CAI-values of all genes of this organism (except genes without an amino acid sequence, e.g. RNAs) devided by the number of genes. This data is also presented in the graphical output of the codon adaptation.Requirements:* Java


Published by: jcat.de
Downloads: 560
File Size: 13.2 MB
License: Freeware
Product Homepage: Visit jcat.de
Release Date: 13 December, 2012
OS: Windows
Download Location: Primary Download Link Broken? Report it!


JCAT (Java Codon Adaptation Tool) 1.0 Download Tags:
Codon Usage    Bias    Adaption    Bioinformatic    Prokaryotes    Transcription    Terminator

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