Prosite Menu

 

• Find (or ⌘-F)

This menu command is only available if
   -  a sequence file is open,
   -  a pattern database file is open and the corresponding window is the active window, 
      and
   -  at least one pattern is selected from the list of patterns.

When this command is chosen MacPattern begins to scan the sequence file for any occurrences of the selected patterns. A rotating wait cursor and a small window with a progress bar indicate the progress of the search. 

This window is a movable modal dialog. That is, you can move it around the screen, but you cannot use any other option of MacPattern during a search. Most importantly, it allows you to switch to another application by clicking on a window which belongs to that application, by clicking on the small icon in the right upper corner when you are running System 6 and MultiFinder or by selecting an application from the Application menu in System 7. If you switch to another application, MacPattern will continue its search in the background, but will give plenty of time to the active application. When the search is finished, MacPattern will notify you by a beep and by flashing its icon in the left or right upper corner (depending on your System version).

Results are displayed in a results window if there is less than 32,000 bytes of data. Otherwise, a directory dialog box will pop up and you will be prompted for a filename to save the results to disk. 

A search can be interrupted at any time by pressing ⌘-Period or Escape, or by clicking the Stop button.

• Enter Pattern… (or ⌘-E)

Choose this menu command to enter a pattern manually instead of selecting patterns from a database. This command is only available if a sequence file is open. The following dialog box will appear when this command is selected:

You may enter any valid pattern in the standard PROSITE syntax (see Appendix B). MacPattern checks the correctness of the pattern when the Find button is clicked and will notify you if it detects syntax errors.

The Find button starts the search using the currently open sequence file, while Cancel will dismiss this dialog without initiating a search.

Hint: If you want to search a complete protein database for one given PROSITE pattern, you should proceed as follows:

- Double-click on the pattern name in the pattern list to access the documentation.
- Select the pattern in the PA line of this entry with the mouse.
- Use the Copy command to copy it to the clipboard.
- Select Enter Pattern from the Prosite menu.
- Use Paste to insert the pattern into the edit field.
- Click OK.

This way, the search will be much faster than a search initiated by selecting one entry in the pattern list. 

• Sort Results by Pattern and Sort Results by Location

These menu commands are used to select the format in which the search results are arranged. The currently selected option is indicated by a check mark.

If you choose Sort Results by Pattern, then any hits will be grouped by patterns, in the order in which the patterns occur in the pattern database:

If Sort Results by Location is selected, output will be sorted according to the occurrences of patterns along the sequence:

Regardless of which method you choose, sorting is performed for each input sequence independently if there is more than one sequence in the sequence file.

Changes of the sort method come into effect for following searches only. Search results already shown on the screen are not affected when the sort method is altered.

• Show Entry Name and Show Accession No

These commands control the way a pattern database file is displayed in a database browser window. The currently selected option is indicated by a check mark.

If Show Entry Name is chosen, the entry name of each database entry is shown in the browser. If Show Accession No is selected, the corresponding accession number is shown instead. Changes of this parameter come into effect immediately and affect all pattern database browser windows currently open as well as those that will be opened afterwards.