Setting the origin

Resetting the origin for circular sequences

Sometimes, for example when you have used the Cloning Clipboard to create a new construct, the physical origin is not correct. That is when you view a circular sequence in the Editor the start and and of the sequence does not correspond to the origin.

For example if you want to remove a restriction site from a sequence you can digest with that enzyme, blunt the fragment and then circularize it. The resulting sequence will have the origin to be the location of the removed restriction site.

To change the origin:

1. Select the place in the Sequence Editor where you want the origin to be (i.e. where it was before the digestion/ligation operation).
2. Right click (or hold down CTRL and left click).
3. You will see a menu that contains a new tool called SET CIRCULAR ORIGIN. Use that to reset the origin of the sequence.

Changing sequence numbering

As well as changing the physical origin of a circular sequence you can also change the numbering of all sequences. The plus origin of the sequence is indicated by a small red plus sign above the sequence in the Editor. MacVector allows you to set the origin of the sequence to be a location other than the beginning or end of the sequence, so that you can conform to the negative numbering system often used when referring to sequence data upstream from some significant feature. To set the plus origin, place the pointer over the plus sign, hold down the mouse button, and drag the plus sign to the residue that you want to be number 1. The sequence numbering is adjusted accordingly, and the numbers of features in the features table are also adjusted to reflect the new origin.

Sometimes when working on a small subsequence of a much larger sequence it is easier to take that section and make a new file. It is also generally useful in such circumstances to preserve the original numbering. For example if you want to analyse a single gene, but still keep the numbering in the context of the full chromosome or genome. With MacVector whenever you copy a section of a sequence then paste this into a new sequence it will preserve the numbering. e.g. if you copy a gene that starts at 1,045 kilobases in the larger sequence, then the new sequence's numbering will start at 1,045,000. To 'reset' the numbering just hover the mouse over the red number until it turns into a 'hand'. Then double click and you will be given a dialogue to change the numbering.

Related Topics.

Single Sequence Files

Single Sequence editor

Features table

Annotations

Remove gaps