The normal nine line header for GenBank files need not be present although its presence will not cause any problems as long as the first line of the header is present in its correct format. All EMBL files used need to have the equivalent lines mentioned above. The sequence data itself must be present as lower case characters. The query file used by the program may be either in the GenBank file format or the NBRF-PIR file format. The next line contains a description of the sequence.
Subsequent lines contain the single letter nucleotide codes.
The asteric then appears in the file following the last residue. Details of how to specify the files and select sequences from them are given below. Title - up to eighty characters of descriptive text to label and identify the output. Query sequence file name. A maximum of 131 characters.