Note: This topic is not applicable to BAM-based projects.
The Set Ends dialog allows you to specify that only a selected portion of a particular sequence be used for assembly.
Access the Set Ends dialog by clicking on the Set Ends button from the Unassembled Sequences window.
Enter the endpoints for the range you would like to use in the 5’ End and 3’ End fields.
•Use the Tab key or the mouse to move between fields.
•You may instead enter the endpoints by scrolling with the arrows provided.
•If you need to reset the coordinates to their original values, click on the word Length.
To specify the reverse complement of the selected strand,
click
. This technique can be used to resolve
sense / antisense orientation issues. (See Resolving Sense and Antisense
Orientation.)
To specify the inverse of the selected strand, click
.
Note: The box at the top right of the dialog shows the chosen range in cartoon form. For example, if you chose to specify the complement and the inverse of the selected strand, the cartoon would show an arrow going right to left inside the plasmid. This would indicate that a DNA sequence was the reverse strand sequence, running 5’ to 3’ on the opposite strand.
Note that all sequences are considered potentially circular and sequence ordering begins 5’ to 3’ for the positive strand. Both endpoints are always inclusive, regardless of orientation.