NAME
GD_Reverse_Translate.plVERSION
Version 5.56DESCRIPTION
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.USAGE
-r OR -o must be provided. If both are given the table will be treated as
another organism, named after the table's filename.ARGUMENTS
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 messageCOPYRIGHT AND LICENSE
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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