Should a large amount of data need to be analysed, then it may make sense to customise some of the Jemboss functions to reduce the amount of time used on certain tasks. This information is stored in the
.jembossFavourites file in the home directory and will not be overwritten on installation of a new Jemboss version.
On installation of the Jemboss interface (whether as a standalone or client/server option) the software will generally seek out the home directory (Section 9.3.1, “Local File Management”) of the local computer and save all subsequent files to this folder. There is a difference with mEMBOSS in that the home directory will be a subdirectory of the installation directory bearing the user's username. If the folder location is mis-typed, the error message
No Access to Directory will appear. Hit the
OK button and type the correct location.
Open the local file manager (Section 9.3.1, “Local File Management”) and note the top folder. Typically this will be the username. Access the
Preferences menu on the main Jemboss toolbar and select the
Advanced Options. Note the location of the local home directory path in the middle of the
Advanced Options box and the name of the final folder, it should be the same as the top folder in the Local File Manager (Section 9.3.1, “Local File Management”). Hit the
Create a new folder called
Extra in the local file manager (Section 9.3.7, “New Folder Creation”). Return to the
Advanced Options and enter
/Extra (on UNIX) or
\Extra (on Windows) at the end of the top folder name and hit the
Set button. Hit the
Apply button to close the box. The new home directory will automatically be altered in the local file manager.
Advanced Options box and hit the
Reset button to reset the local home directory to the default setting.
Any directory location on the local computer may be chosen and applied as long as the necessary permissions are in place to allow the user to write to that directory.
Save between Jemboss Sessions option is selected by default. This selection ensures that the local home directory location is retained between Jemboss sessions. De-selection of this box means that the location is reset to the default after the session. Installation of a new Jemboss version should not alter this selection, unless the selected home directory is the same as the system home directory. This is only an issue for Windows machines, and in this case, the home directory will reset to the default Jemboss home directory.
For the Jemboss standalone version (Section 9.2.5, “Local Installation”), there is an option in the
Preferences/Advanced Options to also alter the location of the default working directory (Section 9.3.3, “Working Directory”). This alteration must be
set and will also be
Saved between Jemboss Sessions if this option has been selected.
Favourites menu on the main Jemboss toolbar can hold a sizeable number of programs that are used on a regular basis to allow easy selection.
Go to the
Protein menu on the left hand side of the Jemboss pane and select the
helixturnhelix program from the
2D Structure submenu. Select the
Favourites menu from the main Jemboss toolbar and click on the
Add to Favourites option. Re-open the
Favourites menu and note the new program addition at the bottom of the list.
Programs are added to the list using their one line description with the program name in parentheses.
Favourites/Edit Favourites option and hit the
Delete button to the right of the
eprimer3 program. Hit the
OK button. Re-open the
Favourites menu to note the disappearance of
Favourites/Edit Favourites option and alter the
helixturnhelix program to
antigenic using the alphabetical drop down menu. Delete the
helixturnhelix description from the text field to the right of this menu and type
Find Antigenic Regions instead. Hit the
OK button. Re-open the
Favourites menu to note the new program description.
The description of a program does not alter automatically when the program is altered from the drop down menu, so care must be taken to avoid altering one and not the other.
The new list is automatically saved between Jemboss sessions. Once the list has been altered it remains that way and will not automatically return to the original list. The contents of this
Favourites list are stored in the
.jembossFavorites file on the desktop computer.
Should the same sequence be required for analysis by several different programs, it can be set as the default.
Sequence List option from the
Tools menu on the main Jemboss toolbar. Left click on the top
File/Database Entry field to highlight it, type
uni:bgal_ecoli and hit return. The
Tools/Get sequence lengths automatically option, when checked, will display the start and end of the sequence (retrieval of this information may take a few seconds). Click with the left hand mouse button on the right hand
Default box to select a sequence as the default option. Close the Sequence List window.
All sequence files or USAs may be added to the sequence list. If the added file is a listfile then the
Listfile option should be selected. Any number of files may be added to the sequence list, and they can be dragged and dropped into the file input field (Section 188.8.131.52, “File/Database Entry”).
Note that the
Get sequence lengths automatically option does not work retrospectively, it must be selected before an entry in the File/Database Entry is made. This option is invalid when the input file is a listfile.
The sequence list will be saved within the same Jemboss session (whether the window is closed or not) and can be saved between Jemboss sessions by selecting the
Save Sequence List option from the
Tools menu. This creates a
.JembossSeqList file on the local computer containing details of the saved list.
Additional rows in the table can be created using the
Tools/Add Sequence option.
Rows (empty or full) may be deleted using the
Tools/Delete Sequence option. Highlighted rows are deleted individually.
emma by typing
emm into the left hand
Go To field and hitting return. Tick the first box under the
LOAD SEQUENCE ATTRIBUTES bar to select the
Only produce dendrogram file parameter.
This greys out all those parameters which are now no longer required for the analysis run.
Advanced Settings from the main Jemboss menu and de-select the
Shade unused parameters option at the top of the box. Hit
Place the cursor in the
Go To field and hit return to reselect the
emma program and reset the parameters. Re-select the
Only produce dendrogram file parameter and the unavailable parameters will disappear.
To reset to default, the Advanced Settings must be manually altered.
All programs that offer a textual output produce results contained in a Text Editor (Section 184.108.40.206, “Text Editors”) window. The view within this window may be altered by changing the size and format of the text using the drop down menus on the toolbar. Use the colour menu to alter the colour of the text and background.
None of these changes can be saved, and they alter the current view only.
The Job Manager (Section 9.6.3, “Job Manager”) is set by default to update every 15 seconds. This can be altered in the
Preferences/Advanced Options box by selecting an alternative interval from the drop down menu next to the
Job Manager Update Frequency option.
An analysis run depends on the input parameters as well as the sequence attributes and EMBOSS programs will calculate this on the fly for each analysis. De-selecting this option in the
Preferences/Advanced Options section allows an analysis to be run without this automatic calculation. This may be useful for testing an analysis and allows the user more control over the workings of the program.
To alter the proxies (Section 9.2.11, “Proxies”) and/or server settings, access the
Settings options from the
Preferences menu on the main Jemboss window.
For the Jemboss standalone version (Section 9.2.5, “Local Installation”) the option is to set a browser proxy. Select the
Use proxy settings for HTTP browser connection and type the correct proxy address into the
Proxy field. Add the
Proxy port number in the second field. Hit the
OK button to verify.
For the Jemboss client/server version (Section 9.2.6, “Remote Installation”), both browser proxy and proxy settings can be altered as for the standalone version. In addition, the location for the remote server can be altered by setting the correct name and address for the Public and Private servers. Hit the
OK button to verify.