Blocks Menu

 

• Search (or âŒ˜-B)

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

When this command is chosen MacPattern begins to scan the sequence file for segments that produce high scores when matched with the selected blocks. A rotating wait cursor and a small window with a progress bar indicate the progress of the search. See the Find command from the Prosite menu for details.

• Search Options…

This command opens a dialog box which allows you to set the number of high-scoring blocks per sequence to display in the search output and to adjust the search sensitivity.

In the first edit field, enter the number of high-scoring blocks you want to see. Then select whether you want to do exact searches or approximate searches. In the latter case, enter a value for the sensitivity threshold. The lower this value is the faster the search will be but sensitivity will decline as well (see chapter ‘Algorithms’ for details). Click OK, or click Cancel to leave the dialog without changes.

• Show Entry Name and Show Accession No

These commands control the way a block 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 block database browser windows currently open as well as those that will be opened afterwards.