Hi there,
The issue with circular molecules has been in the forum for some time. I would like to add something to this subject.

Whether a molecule is circular or not can be considered in the cloning menu (digestion into fragments) and when a sequence is analyzed for restriction enzyme cut sites. However, in other circumstances there is no option to consider the sequence as circular. Namely when I want to select a sequence region which goes over the start and end point. For example I have an annotated plasmid (circular sequence) with 6000 bp. I want to select the region from 5000 to 1000 (->2000 bp long). To my knowledge this is not possible. When I do "multiple range selection" with the two parts of the sequence and copy and paste the sequence in an editor, they are added the wrong way round (linear sequence, first the subsequence from 1 to 1000, then the sequence from 5000 to 6000). When I want to preserve the annotation and export the subsequence in gb-format, it gets even more complicated to fuse the two parts of the sequence in an editor while preserving the annotations at the right positions.
When I want to use the option "cloning -> create fragment" there are the same problems, as with "select sequence region".
So here is my suggestion: Whether a sequence is circular or linear is a physical property of this sequence, therefore there shouldn't be a button "consider the sequence as circular" in all of the feature menues, but a button in the sequence viewof each sequence, whether the sequence IS circular or not (perhaps a button next to the button for "show circular view"). I think this would make sense, as it would be more object oriented. Perhaps it is possible to save in the annotations or as a remark in the gb-format, wheater a sequence is circular of linear.

If this was implemented, it would be cool, if the following worked: "select sequence region" and then select from 5000 to 1000.

Onother suggestion: If I want to mark a sequence with 1000 bp with the mouse in the sequence details view, this is very tiering, as the window moves so slow, when the mouse is drawen to one side of the window. Perhaps the scrolling speed could be made dynamic, so that also large subsequences can be selected by holding the left mouse button pressed.

Cheers to you and thank you for this great program, Ugene!
Thomas

Dear Thomas,

thank you for your suggestions. I've created an issue(https://ugene.unipro.ru/tracker/browse/UGENE-1354) to implement the feature with circular molecule.
We had an option to select ranges like 5000..1000. But it was broken. We'll fix it in the coming release.
Let me see if we can implement the speed up when scrolling in sequence view.

I totally agree with the comments. Please, have also in mind this forgotten issue:
https://ugene.unipro.ru/tracker/browse/UGENE-777

That could serve as a workaround to the problems of selecting sequences around the starting point.