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The MTDR Calculator

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Brief review:

The Mean of the Typical Decoding Rates (MTDR) calculator enables calculating the translation efficiency index of different genes. This index1 calculates the geometrical mean of codons translation efficiency, which is based on a new analysis method of ribosomal profiling data. Specific values of codons decoding times of different organisms appear here.

 

ORFs can be provided both in FASTA format or in a text file (each ORF in a separate line). See input examples here (FASTA, text).

 

A detailed guide can be downloaded here.

 

Installation instructions:

 

·           Download MTDR calculator from here: MTDRcalculator.jar

·           To run the application you need to install a Java virtual machine (JRE). You can download one from Sun's Java web site or contact your OS manufacturer.

·           After downloading the MTDR calculator please double click on the MTDRcalculator.jar file to run the MTDR calculator.

 

 

 

 

 

 

When you use the MDTR calculator please cite:

 

1.         Dana A. and Tuller T. The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res. 2014 (pdf, Supplementary pdf)

2.      Dana A. and Tuller T. Mean of the typical decoding rates: a new translation efficiency index based on ribosome analysis data. 3G. 2014 (pdf)