Staden: Translating and Listing Nucleic Acid Sequences

This chapter deals with producing simple listings from nucleotide sequences. All functions are contained in the program NIP. Sequences can be listed alone, in single- or double-stranded format, or with translations to protein. The translations can be of all six phases, all open reading frames, or of specified segments. The positions of these segments can be defined on the keyboard or read from a EMBL/GenBank feature table. Translations can use the one-letter or three-letter codes. In addition, files can be produced containing only the protein translations and which are suitable for processing by other programs. Again, the positions of the translated segments can be defined on the keyboard, read from a feature table, or be all open reading frames. For the user, producing all these results is very simple, so only examples of “methods” are given and what the results look like is shown. All outputs that list the sequence can be produced from the menu option named “Translate and list.”