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prodoric is a simple Perl script to access the PRODORIC webserver for bacterial promoter analysis. It takes a FASTA file as input and produces a CSV file summarizing the results.

By default it looks for E. coli transcription factor binding sites, but options allow you to select other species or all species. Other options allow you simply to obtain a count of the number of sites found, or of unique sites found and to specify a threshold for the confidence score provided by PRODORIC.

Download and Install

Simply download the script and place it in your path. Make it excutable by typing:

   chmod +x prodoric.pl

Download prodoric.pl


Run the program with the -h flag to get help. If you have placed the program in your path simply type:

   prodoric.pl -h

If the code is in your current directory instead and the current directory is not in tyour path, then type:

   ./prodoric.pl -h