Sip allows more than two sequences to be available to the user but only two are "active", that is, to be used in the comparison routines. The active sequence is changed using the "Sequence manager" option in the "View" menu. This command invokes a list box showing all the sequences which have been read into SIP together with their lengths and whether they are DNA (D) or Protein (P). The currently active horizontal and vertical sequences are marked with a "H" and "V" respectively. In the picture below, these are "hsproperd" and "mmproper".
![[picture]](sip_seq_manager.gif)
There are several operations which operate on a single sequence and these are available from a popup menu within the sequence manager.
Clicking on the sequence name with the right mouse button invokes a pop-up menu containing operations which may be performed on that sequence. The operations available depends on whether the sequence is DNA or protein.
These options are described in greater detail below.
To change the current active horizontal or vertical sequence, select the sequence and invoke the pop-up menu by pressing the right mouse button. Select "Horizontal" or "Vertical" from the pop-up menu. This sequence will now be the active "Horizontal" or "Vertical" sequence.
This function will reverse and complement nucleic acid sequences. Select the "Complement" command from the pop-up menu. A new sequence will be added to sequence manager list box with the same name as the parent but with "_c" appended to the end. The third entry in the picture above is the complemented sequence of "hsproperd".
This operation is only available for DNA sequences. Select the "Translate" command from the pop-up menu. It is possible to translate in any particular frame by selecting the appropriate check box. For each translation, a new sequence will be added to the sequence manager list box with the same name as the parent but with the addition to the end of either "_rf1", "_rf2" or "_rf3" to signify reading frames 1, 2 or 3 respectively.
It is also possible translate all three frames at once using the option "all frames separately" which will produce three new sequences in the sequence manager. The forth to sixth entries in the picture above are the three reading frames of "mmproper".
Finally, the "all frames together" option will produce a single new sequence in the sequence manager, with the extension "_rf123", exemplified by the seventh entry in the picture above. Although at this point the sequence is still DNA, the use of this sequence in a comparison function will translate it automatically into the three reading frames.
For example to compare a DNA sequence in all it's reading frames with a protein:
This function produces a version of a given DNA or protein sequence in which the characters are randomly reordered. i.e. the new sequence has the same length and composition as the original but with the characters in a random order. The new sequence will be added to the sequence manager list box with the same name as the parent except with "_s" appended to the end. The eighth entry in the picture above is the scrambled version of "hsproperd". For long sequences, scrambling and then comparing should produce similar numbers of matches as are predicted by the probability calculations ( see section Probabilities and expected numbers of matches).
To save a sequence to a file, select the "Save" option from the pop-up menu. This command invokes a file name entry box. The browse button to the right of the dialogue box invokes a filebrowser See section `Introduction' in filebrowser. The sequence is written as plain text.
To delete a sequence, select the "Delete" option from the pop-up menu. This command will remove the sequence from the sequence manager and all plots and results that were produced from it.