Create Representative Genome Server Directory

p3-rep-prots.pl [options] outDir

This script processes a list of genome IDs to create a directory suitable for use by the RepresentativeGenomes server. It will extract all the instances of the specified seed protein (usually Phenylanyl synthetase alpha chain) and only keep genomes with a single instance of reasonable length. The list of genome IDs and names will go in the output file complete.genomes and a FASTA of the seed proteins in


The positional parameter is the name of the output directory. If it does not exist, it will be created.

The standard input can be overriddn using the options in Input Options.

Additional command-line options are those given in Column Options plus the following options.


The description string of the desired protein role. The default is Phenylalanyl-tRNA synthetase alpha chain.


The minimum acceptable length for the protein. The default is 209.


The maximum acceptable length for the protein. The default is 485.


Clear the output directory if it already exists. The default is to leave existing files in place.