GD_Reverse_Translate.pl
Version 5.56
Given at least one protein sequence as input, the Reverse_Translate script generates synonymous nucleotide sequences using either a user-defined RSCU table or an RSCU table provided by GeneDesign 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 the suffix _RT. 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.
-r OR -o must be provided. If both are given the table will be treated as another organism, named after the table's filename.
Required arguments:
-i, --input : a file containing protein sequences. -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, or several separated by commas -r OR -o must be provided. If both are given the table will be treated as another organism, named after the table's filename.
Optional arguments:
-a, --algorithm : protocol for replacing peptides; defaults to "balanced" -out, --output : path to an output directory; defaults to GeneDesign's default -f, --format : default genbank -s, --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:
* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
* The names of Johns Hopkins, the Joint Genome Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the GeneDesign developers may not be used to endorse or promote products derived from this software without specific prior written permission.
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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.