Hello! Could you please help me:

I've loaded gbk file with complete genome annotation into Ugene. After that I've found a pattern in genome - it is stored in a new annotation group. Is it possible to select patterns that overlap with CDSs and those that lie in the intergenic regions separately?

Many thanks,
Olga

Hello! Thank you for your request!

To manually distinguish the pattern annotations you can do the following:
1) Look at the Sequence Zoom View and pay attention to the regions where CDS annotations are located - see the screenshot.
2) Move all annotation into one folder and sort them by the location value. Then, go through the annotations and manually move the required intersected annotations into another folder.

Alos, you might like to participate in a UGENE webinar. In this case I will show you these features in details and other useful features as well.

I've also created an issue in our tracker system (UGENE-3703) to automate the described procedure with the workflow sample .

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I believe all such requests concerning automated manipulation of annotations and so on can be performed by full support of bedtools in UGene. If it was possible to perform bedtools operations on UGene objects (annotations), it would be an invaluable feature.

Ilya, I've create UGENE-3808 for your request.

Actually, would be nice to be able to use bedtools and similar toolsets in workflow editor (and a separate tools in UGene too), and I think the idea of using bedgraph/wig and similar files in UGene to plot graphs along the genomic sequences is not novel as well.

Ilya, full bedtools support is actually a good idea. But I think that in the workflow designer it wouldn't be that interesting as it was integrated in the sequence view. I mean it would be much more convenient (for manual analysis) to perform those overlaps/coverage operation for selected annotations in the sequence view. We should think about how to do it nice.

Yuriy, I guess it would be better in the sequence view, I just thought that implementing it in the workflow designer might be easier... And having a way to call bedtools from WD would be very useful - it is a great way to store complicated bedtools piplines. By the way, would be fantastic, if I could call any script/programme that my OS can execute from WD as well.

Ilya, actually you can run any program or script in the WD by creating a custom element. Have you tried this feature?

Note that if it is a script, you should specify the corresponding script interpreter executable file while creating the element, for example, the execution string will be "python myScript myScriptParams".

Great, thank you, I haven't noticed this feature!