In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. The parameters and switches listed below can be set from the command line. This is the same line that is searched in the definition search of the StringSearch program. You can set this identifier to capture whatever line interests you from the heading of your input sequences. If there is no line that starts with your identification token or if you do not use this option, then the first non-blank line in your sequence file is used as the sequence definition.
N sets the type of the dataset to N for nucleic acid datasets, and P for protein datasets.
The type field is stored in the .header file, and used when reading in sequences to set the type of the sequence to protein or nucleic acid. This program normally monitors its progress on your screen. However, when you use the -Default option to suppress all program interaction, you also suppress the monitor. You can turn it back on with this option. If your program is running in batch, the monitor will appear in the log file.