Hello,
I recognised that the auto-annotation of open reading frames does not work if the open reading frame exceeds over the +1 site of the circular sequence (e.g. an ORF of 5100 bp-850bp in a 6000 bp circular plasmid). I was using ugene 1.9.7 portable zip bundle  under windows 7 professional.
It would be very nice If you could fix that bug.
Best regards

Thanks for report!  Will be fixed ASAP.

Issue is created in the bug-tracker:
https://ugene.unipro.ru/tracker/browse/UGENE-662

Hello,
I recognised another issue with circular sequences. Annotations in the .gb file that exceed over the +1 site of the circular sequence (e.g. an annotation of 6917 bp-1651bp in a 6975 bp circular plasmid) are not displayed properly. Instead of the whole annotation, only the first base pair is displayed as an annotation. I was using ugene 1.9.7 portable zip bundle  on windows 7 professional.
It would be very nice If you could fix that bug.
Best regards

Hello,
I've fixed the bugs and all the required functional will be available in UGENE 1.9.8 which will be released soon.

To find ORFs in a circular plasmid the new checkbox "Circular Search" in the "ORF Marker" dialog should be on.

Also the annotation issue has been fixed. In your version you may create an annootation which exceed over +1 site manually in the circular view (select a region - right button click – “New Annotation”). In UGENE 1.9.8 reversed annotations (2000..1000) are considered as straight (1000..2000) and there is no problem with its visualization.

Thank you for your report.

Hello,
I recognised that there is still a bug when displaying annotations in circular plasmids. Annotations in the .gb file that exceed over the +1 site of the circular sequence (e.g. an annotation of 5064 bp to 517 bp in the 5369  bp circular plasmid) are not displayed properly. To demonstrate this I generated an exemplarily .gb file. In ugene 1.10.1, the annotation (Test) is displayed incorrectly as 517 bp to 5064 bp instead of 5064 bp to 517 bp.
It would be very nice If you could fix that bug.
Best regards

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Thanks for noticing that bug.
I've investigated the problem a little bit. Actually, such an attitude to "reversed" regions is beyond format specification. It says that regions should be continious ("Location" chapter in the official specification: http://www.ncbi.nlm.nih.gov/collab/FT/#3.4) and regions that exceed over +1 site should be represented as join(1..517, 5064..5369) in your case (example with D-loop feature here: http://www.ncbi.nlm.nih.gov/nucleotide/169792587?).
But, any way, we will provide you with the feature for circular sequences. I've created the issue: https://ugene.unipro.ru/tracker/browse/UGENE-834 that will be fixed asap.

Hello,
I recognised that the bug is still there. I have got a plasmid (circular) of 5979 bp total length with an ORF ranging from 5976 bp to 2427 bp. However, the ORF is only displayed from the next possible ATG triplet as Ugene does not seem to recognise the start of the ORF correctly. It should be clear that the ribosome does not see any numbering in circular DNA and will just read the first AUG on the mRNA after the RBS. If you use ugene's own cloning pipeline in order to create a virtual plasmid containing a protein to be expressed, it usually produces a small part of the ORF to be at the other end of the plasmid sequence. Therefore, it is crucial to fix this bug.
Many thanks in advance.

Hello!
Thank you for an additional info. For now this issue of a high priority (https://ugene.unipro.ru/tracker/browse/UGENE-1709). We will make not only the ORF finder, but also the other algorithms aware of the circularity of a sequence.