Genome Analysis Software Info Site

Registering a base sequence pattern

• Clicking the Pattern Registration button (□) (Bxx) opens the Pattern Registration dialog (Dxx).
• In this Pattern Registration dialog (Dxx), you can register one base sequence pattern at a time by giving it a unique name (pattern name).
• If you register a pattern name that has already been registered, an overwrite warning message (MSGxx) will be displayed asking if you want to Overwrite it.
• If you answer Yes, the previously registered pattern will be overwritten.
• If you answer No, the Pattern Recognition dialog will remain displayed, so change the pattern name to something unique and press the Save button (Bxx).
• You can also copy and paste patterns from other sources.
• You can also drag and specify a base sequence in the IMC main window (W1) and register it directly as a base sequence pattern.
• If you drag the mouse cursor to any position on the base sequence (either strand can be specified) displayed in the IMC main window (W1), the area will change to a pink shaded area.
• Click the right mouse button to display a pull-down menu.
• In that menu, there is a menu item called PatternRegistration (MExx). Click the left mouse button to display the Pattern Registration dialog (Dxx),
• in which the shaded area is displayed as the pattern.
• Enter a unique pattern name here and press the Save button (Bxx) to register the base sequence pattern.

Saving registered base sequence patterns

• The base sequence patterns registered using the Pattern Registration dialog (Dxx) are saved in the setting file (Fxx) when IMC is closed.
• The next time IMC is started, this setting file (Fxx) is automatically loaded, so the registered base sequence patterns will be saved unless you intentionally delete them or change the system operating environment.

Deleting registered base sequence patterns

• A base sequence pattern that has already been registered can be deleted at will in the Pattern Match dialog (Dxx), which is displayed when you press the Pattern Match button (Bxx).
• The Pattern Matching Dialog (Dxx) displays a list of all registered base sequence patterns. Check the USE checkbox of the pattern you want to delete and click the Delete button (Bxx) at the bottom of the Pattern Matching Dialog (Dxx). All checked patterns will be deleted.
• At this time, a deletion confirmation message (MSGxx) will be displayed.
• If you answer Yes, the deletion will be executed, the deleted base sequence pattern will be removed from the list, and only the remaining base sequence patterns that were not deleted will be displayed.
• If you answer No, the deletion will not be executed and the Pattern Matching Dialog will remain displayed.

Searching DNA sequences using registered patterns

• Right-click the Pattern Matching button (Bxx) and select one or more base sequence patterns you want to find from the SelectPatten list (Lxx) in the Pattern Matching Dialog (Dxx).
• Selection is performed by right-clicking the USE checkbox to check it.
• Right-clicking another item will invert the item, but this does not mean it is selected.
• If you want to use all the base sequence patterns in the list, right-click the AllSelect button (Bxx) at the bottom and all the patterns will be checked.
• If you want to exclude some patterns from the list and select all the remaining ones, first check the patterns you want to exclude (multiple patterns are possible), then right-click the
• Reverse Selection button (Bxx). Check marks will be removed from patterns that were previously checked, and check marks will be added to patterns that were not checked.
• In other words, this button reverses the marked patterns.
• If you right-click the Search button (Bxx), a pattern search will be performed for all base sequences.
• The search is performed for a perfect match with the pattern, but the following base sequence codes can be used at this time, so incomplete match searches that allow mismatches are also possible.

Nucleic acid notation code

Table is inserted

Display of base sequence pattern search results

• When the search is completed, the results will be displayed in the Pattern Match Site Window (Wxx).
• All the locations where the pattern was found are listed, one line per location.
• If you right-click on a line in the displayed list, the base sequence including the position on the DNA sequence where the pattern indicated by that line was found will be displayed in the base sequence display area, and the area where the pattern matches will be displayed in a colored shaded area.
• In addition, the base sequence position indication line cursor will also move in the FK display area. Clicking on another line will jump to that pattern position.

Saving the results of base sequence pattern search

• Right-click on the check box of any line in the base sequence pattern search result list to check the check box, and then right-click on the Save button (Bxx) at the bottom to save the checked position, the gene names (GeneName) before and after it, and the base sequence around it as a file in CSV format.
• This file can be read by software such as a text editor or EXCEL.
• In addition, this file can be used to analyze the characteristics of base sequence similarity regions.

Registering the base sequence pattern search position as a feature key (FK)

• The matching position found as a result of the pattern search can be registered as a new feature key (FK).
• Check any line of the discovered pattern position and right-click the FK registration button (Bxx) at the bottom. The feature key registration window (Wxx) will be displayed. Right-click the
• Save button after setting values ​​for the necessary items to set FK information for all positions at the same time.
• The position information cannot be changed in this case, but once registered, you can change the position by resetting the feature key for each position.
• For details on this function, see the section on new and updated feature key registration.

Limiting the base sequence pattern search area

• The base sequence pattern search function allows you to limit its range.
• First, if you want to limit the search to only the leading strand, select the search direction (Direction) before pressing the Search button (Bxx).
• The default is to search both strands, but if you want to search only one strand, right-click either the Forward or Reverse button and specify the search area.
• If you want to limit the search position, specify the search start base position (From) and search end base position (To) before searching.
• Even when searching the complement strand, set the From position to the left (less than) the To position.
• In this case, if you search a very large DNA sequence with a short base sequence pattern, the matches found will be very long, so in such cases we recommend that you limit the range before running the search.