Note: This topic is not applicable to BAM-based projects.
SeqMan Pro can remove specified vector sequences during the preassembly process. To scan for vector, first choose from one of the following three scenarios:
If you have a smaller number of reads and up to two vectors:
1) Highlight the name(s) of the sequence(s) to scan in the Unassembled Sequences window. Select multiple files by using Ctrl+click (Win) or Cmd+click (Mac) or Shift+click or select all sequences by selecting Edit > Select All.
2) Select a single vector using one of the Vector pull-down menus or select two different vectors by using both menus. The vector(s) you choose will appear in the “Vector” column, with a ? to the left. This symbol indicates that a vector has been selected, but the sequence in question has yet to be scanned. Note that different vectors may be chosen for different sequences.
If you have a large number of reads and want to specify multiple vectors you may prefer to specify a single vector for each read:
1) Sort your data into separate groups using Windows Explorer or the Macintosh Finder.
2) Use drag and drop to add sequences for the first vector to the Unassembled Sequences window.
3) While the sequence names are still highlighted, select a vector using one of the Vector pull-down menus. The vector you choose will appear in the “Vector” column, with a ? to the left. This symbol indicates that a vector has been selected, but the sequence in question has yet to be scanned.
If you want to trim all sequences for multiple vectors:
1) Select all of the sequences in the Unassembled Sequences window by selecting Edit > Select All.
2) Select the first two vectors from the Vector pull down menus. The vectors you choose will appear in the “Vector” column, with a ? to the left. This symbol indicates that a vector has been selected, but the sequence in question has yet to be scanned.
3) Scan and remove vectors as directed below.
4) Assign additional vector(s) to each sequence and trim again.
Once you have selected the vector(s) for one of the scenarios listed above, you are ready for SeqMan Pro to scan and remove the vectors:
1) Click the Options button to open the Preassembly and Assembly Options dialog.
2) Select Scan for Vector.
Note: The Scan for vector selection can only be made after a vector is assigned.
3) Choose from one of the following options:
Click Scan Selections to trim vector now from selected sequences only.
Click Scan All to trim vector now from all sequences.
Click Scan Later to postpone vector scanning until clicking the Assemble button.
SeqMan Pro removes vector sequence by first aligning each constituent sequence against the vector cloning site region and then excising vector matches within the constituent fragment sequence.
Any vector trimming updates the Limits column in the Unassembled Sequences window.
After vectors have been removed, the “Vector” columns in the Unassembled Sequences window are updated with post-scan symbols:
¿ indicates the vector was not found in the sequence
√ indicates vector sequence has been found and removed
∅ indicates that the whole sequence was vector and will not be used in assembly
Note: The ? symbol indicates that a vector has been selected, but the sequence in question has yet to be scanned.
To see data that has been removed from a particular sequence due to vector trimming, select the sequence and select Sequence > Show Original Trace/Flowgram Data. In the Trace Data window, a red arrow labeled “Vector” and red vertical bar marks the location of any vector trim site. Note that the Trace Data and Flowgram windows are disabled for BAM-based projects.
Hint: If you use the same vector most of the time, you may want to specify it as the default vector.