Entries may be added to a subsequence file at any time that the window for the file is active.
1. Open the required subsequence file, and ensure that the file window is active.
2. If the file is locked, unlock it by toggling the lock button.
3. Select the button labeled with a plus (+) sign.
The Subsequence Editor dialog box is displayed.
4. Type a name for the subsequence in the Name text box.
5. Select the No. of parts radio button that corresponds to how many parts the subsequence will have.
6. In the Part # text boxes, type the sequence for each part of the subsequence, using standard IUPAC one-letter codes.
NOTE: Use parentheses to enclose a combination of amino acids for an ambiguous residue. For example, if either an aspartic (D) or glutamic (E) acid residue can occur at a given position, denote it as (DE).
7. Use the Perfect Match and Allowed mismatch text boxes to adjust the tolerance of the match as follows:
- to specify an exact match, type 0 in Allowed mismatch and leave Perfect match empty
- to allow some degree of mismatching, type the maximum number of mismatching residues that you will accept in the Allowed mismatch text box
- to require that specific residues match exactly, type X beneath those residues in the Perfect match box, using spaces to position the Xs. For amino acid motifs, only one X can be placed beneath each group of amino acids enclosed in parentheses. The allowed mismatch cannot exceed the length of the sequence for that part of the subsequence.
8. If you want to add an offset to the reported position of the subsequence when a search is performed, type a value in the Offset text box.
usually, the number of the first residue in the subsequence is reported.
9. If required, you can enter a comment up to 254 characters long.
10. For subsequences with more than one part, you can treat each part of the subsequence as if it were a separate motif:
- select the Logic: or radio button to report a subsequence found if any combination of the subsequence parts is found
- select the Logic: and radio button to report a subsequence found only if all subsequence parts are found.
11. For subsequences with more than one part, select one of the Offset part: radio buttons to report the position of the subsequence relative to any of the parts.
This option appears only if you are using AND logic. It is used in conjunction with the Offset value. If you select 1 as the offset part and type 0 as the offset, MacVector will report the position of the first residue of the first part of the subsequence. If you select 3 as the offset part and type 4 as the offset, MacVector will report the location of the subsequence to be the fifth residue of the third part of the subsequence.
12. For subsequences with more than one part, use the Gap text boxes to specify the limits on the number of residues that may occur between each part of the subsequence.
This option appears only if you are using AND logic. For example, if your subsequence consists of two parts which may be separated by 10 to 20 residues, you would type 10 and 20 in the #1 - #2 Gap text boxes. The gap values may be any number from zero upwards, and the second number must be equal to or larger than the first.
13. Select OK to add the subsequence to the file.
14. Choose File | Save to make the changes permanent.
Copying existing entries between files can be useful, for example to create a customized subsequence subset from more than one file. One or more subsequence files must be open at the same time, and the file receiving the subsequence entries must be unlocked.
1. Make the file from which you are copying entries the active window.
2. Select the subsequences that you want to copy:
- click to select a single entry
- hold down the mouse button and drag to select a continuous block of entries
- hold the shift key in combination with either of the above to retain already selected entries
3. Choose Edit | Copy.
4. Make the file that is receiving the entries the active window.
5. If the file is locked, unlock it by toggling the lock button.
6. Choose Edit | Paste.
The entries are added to the file in alphabetical order.
7. Choose File | Save to make the changes permanent.
If any of the entries were marked as selected (with a check mark), the selection will be retained.
Entries in a subsequence file can be modified. This is generally useful only when a mistake has been noticed in the existing entry.
1. If the file is locked, unlock it by toggling the lock button.
2. Select the button labeled with a delta sign.
The Subsequence Editor dialog box is displayed.
3. Modify the entry as required.
4. Select OK to add the changes to the subsequence file.
5. Choose File | Save to make the changes permanent.
Entries in a subsequence file can be deleted when required.
1. If the file is locked, unlock it by toggling the lock button.
2. Select the subsequences that you want to delete:
-click to select a single entry
-hold down the mouse button and drag to select a continuous block of entries
-hold the shift key in combination with either of the above to retain already selected entries.
3. Select the button labeled with a minus (-) sign.
The selected entries are deleted from the file.
4. Choose File | Save to make the changes permanent.
NOTE: This is equivalent to using Edit | Clear. If you want to paste the deleted entries into another file, use Edit | Cut instead of the minus button.
Searching for nucleic acid subsequences
Filtering nucleic acid subsequences results
Displaying nucleic acid subsequence results