When the ending position is set from the command line, DataSet ignores ending positions specified for sequences in a list file. This is the same line that is searched in the definition search of the StringSearch program. For EMBL format the line begins with DE . 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 parameter, 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. Peptide sequences representing translations of the three forward reading frames are designated with the original entry name followed by f1, f2, or f3 while those corresponding to the three reverse reading frames have names containing r1, r2, or r3. However, when you use -D efault to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.