GD_Juggle_Codons.pl
Version 5.56
Given at least one protein-coding gene as input, the Juggle_Codons script can use several algorithms to modify the sequence without altering its translation. It is thus possible to generate a sequence that is optimized for expression, as different as possible from the original sequence, or some combination of the two. If no algorithm is specified, the balanced algorithm will be used. These are the algorithms provided by default with GeneDesign; you can make your own; see developer docs. Output will be named according to the name of the input file, and will be tagged with _CJ. Algorithms: high: The high algorithm replaces every codon in the input sequence with the most translationally optimal codon as specified by the input RSCU tables or known RSCU tables (if organism is specified). If the codon is already the ideal codon it is left alone. balanced: The balanced algorithm uses the rscu data to determine a likelihood of codon replacement. most_different_sequence: The most different sequence algorithm attempts to change as many bases as possible within the codon, preferring transversions over transitions. least_different_RSCU: The least different RSCU algorithm attempts to replace as many codons as possible while minimizing disruption of the original average RSCU value for the sequence. It will not make a replacement if the absolute change in RSCU value is greater than 1. random: The random algorithm makes random replacements.
-r OR -org must be provided. If both are given the table will be treated as another organism, named after the table's filename. Generate high and most different sequences given the yeast rscu table ./GD_Juggle_Codons.pl -i sequences.FASTA -org yeast\ -a most_different_sequence,high Use my rscu table to generate balanced sequences ./GD_Juggle_Codons.pl -i seqs.FASTA -r /my/dir/myrscu.rscu -a balanced Use my rscu table to pipeline balanced sequences ./GD_Juggle_Codons.pl -st ATCGATCCC -r /my/dir/myrscu.rscu -a balanced
Required arguments:
-org, --organism : an organism whose RSCU table can be found in the config directory, or several separated by commas AND/OR -r, --rscu : path to an RSCU table generated by GD_Generate_RSCU_Table.pl
Optional arguments:
-a, --algorithm : which algorithms to use (see above), comma separated defaults to balanced -i, --input : a file containing nucleotide sequences -st. --string : a string containing DNA only - the program will return a DNA only string. this is intended for pipelining. -out, --output : path to an output directory -f, --format : default genbank -sp, --split : output all sequences as separate files -h, --help : Display this message
Copyright (c) 2015, Sarah Richardson All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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To install Bio::GeneDesign, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::GeneDesign
CPAN shell
perl -MCPAN -e shell install Bio::GeneDesign
For more information on module installation, please visit the detailed CPAN module installation guide.