The necessary file for completion of this tutorial is available on our FTP site. Please feel free to download it. If you are using Windows, highlight the file you want and click on it with your right hand mouse button. Select the "Copy to Folder" option to copy the file to your local PC. Linux users need to click on the link for the appropriate file and the download manager will do the rest. Save the files to your Demo folder or the one you specified in the File Manager Tutorial.

You will need the file:

• pax6_human.swiss

Select the Sequence List option from the Tools menu at the top of the Jemboss window. The default list will open.

On opening, the sequence list contains space for five sequences. This can be extended to further accomodate as many sequences as necessary. This list can be populated with sequences in a number of ways.

Highlight the first row and into the File/Database Entry box type uniprot:O97929. Fill in the Start and End positions of the sequence by selecting the appropriate field and double clicking to place the cursor into it. Type 1 and 65 as the start and end positions of the sequence.

Open the file manager and drag pax6_human.swiss into the second entry box in the list. Leave this entry highlighted, open the Tools menu on the Sequence List window and select Calculate Sequence Attributes to see the sequence length.

If you are using MS Windows, there is a chance that the Sequence List will appear as a window overlapping the Jemboss window. When the sequence in the Jemboss file manager is accessed the Jemboss window will move to the front completely obliterating the Sequence List. If this is the case, it will be necessary to move both windows until the row you wish to drag your sequence into remains on display even when the Jemboss window is in front.

The calculated sequence attributes automatically fill in the start and end points of the sequence.

On addition of a sequence dragged in from the file manager, an additonal row automatically appears in the List tool, thus extending the scope of the list. Should no files be dragged in, but there is a requirement for more than five sequences, rows may be added separately.

Add in a couple of rows by using the Add Sequences option in the Tools menu. Additonal rows will appear in the List. Delete these rows by highlighting each one and selecting the Remove Sequences option from the Tools menu.

Check the Default box for the pax file.

Checking the default means that whenever a program requiring a sequence file as input is opened in the main Jemboss window, this chosen file will already appear in the input field.

Go to the Favourites menu and select Pattern Search (Protein). The default sequence selection will appear in the file input field ready for a protein pattern search.

Repeat this process with Pattern Search (nucleotide) and the same default sequence will appear. This time it is not appropriate as we cannot do a nucleotide pattern search using a protein sequence.

Currently the program does not differentiate between a nucleotide or protein sequence file and thus it is important to make sure that any file set as default is appropriate for the program it will be used for. Defaults may be altered at any point during the session. At the moment, the sequence list will not store more than one default file.

Sequences need not be made to appear as the default every time you load a program. They may be dragged from the sequence list into the relevant program form instead. However, should you require that the same sequence be made available for multi-analysis, then a default selection may be appropriate.

Return to the sequence list and select the Tools menu once more. Check the Save Sequence List option.

This selection will ensure that the sequences in the list are saved between Jemboss sessions. At this stage you may close the Sequence List menu.