1- If I export several features as alignments, the sequences I get are the reverse complementaries instead of the originals.

2- Also, I've seen that sometimes you can export the translation of the selected sequences, but that option appears quite seldom. I'm not sure if I'm doing something wrong or if this is a bug.  :-/

Thanks

Agu wrote on Nov 17^th, 2010 at 8:18pm:

1- If I export several features as alignments, the sequences I get are the reverse complementaries instead of the originals.

We'll fix this bug in the next release (1.8.1)


Quote:

2- Also, I've seen that sometimes you can export the translation of the selected sequences, but that option appears quite seldom. I'm not sure if I'm doing something wrong or if this is a bug.  :-/

This could be a bug. The translation is a standard option of any "Export" dialog. (See the image attached) However this option depends on the alphabet. The option is not visible if the sequence alphabet is detected as Raw or is not set by some reason.

Could you please describe a situation when this is option is not shown? What is the format of the file? Was it obtained from specific database or created by some software? If it is created by UGENE what was the pipeline?

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Agu wrote on Nov 17^th, 2010 at 8:18pm:

1- If I export several features as alignments, the sequences I get are the reverse complementaries instead of the originals.

Fixed.
Still wonder why we didn't have tests for these feature before ...

image

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Quote:

Could you please describe a situation when this is option is not shown? What is the format of the file? Was it obtained from specific database or created by some software? If it is created by UGENE what was the pipeline?

Now I figure it out, so I can give a better explanation. My goal was, working with several genbank files in the same display, to select the same feature in the different sequences and to make an alignment. It would be nice to be able to do that for both, DNA and protein.
If I select the different features, I only have the option for a DNA alignment:

http://ugene.unipro.ru/yabbfiles/Attachments/No_selection.png

Now, if I have the Details view activated and select some sequence for both, I get the option for translated alignment:

http://ugene.unipro.ru/yabbfiles/Attachments/Detail_view.png

The "random" behavior came when I had some sequence selected in the detailed view. Even hiding  this views and selecting features, I get the option for translation:

http://ugene.unipro.ru/yabbfiles/Attachments/Selected.png

Then, the problem is that in this last case, Ugene will use the selected features shown in the screen if you choose the DNA alignment, while it will use the "other" selected sequences (hidden or not) when selecting the translation option. This could be solved with an automatic selection in the detail view. I mean, automatically selecting the corresponding sequence in the detail view when selecting a feature in the zoom view. Also, for some situations It would be much faster than having to select a feature and then going to "Select/Sequence around selected annotation".
I can't think of a negative side for that behavior (actually, I believe it would be a nice feature).
Just to make it more clear, after selecting a feature with one click it should look like this:

http://ugene.unipro.ru/yabbfiles/Attachments/automatic.png


Hope this helps...

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Eitel,
you can select sequence around annotation automatically by using Ctrl + Mouse Click on it. I've just discovered that we don't have this useful feature documented. We will consider having this mode as default.

Looks like having selected both annotations and sequence regions might be a little bit confusing. There is no option to make alignment from the translated sequences of selected annotations, thus only option for selected sequence regions is shown and it's named not very clearly. We will add the same functionality for selected annotations and think on how to improve overall design of this feature.

This could be solved with an automatic selection in the detail view. I mean, automatically selecting the corresponding sequence in the detail view when selecting a feature in the zoom view

Fixed. Now with every annotation selected a sequence region around the annotation is also selected, so you have 2 sets of options: work with annotation selection or with sequence selection independently



My goal was, working with several genbank files in the same display, to select the same feature in the different sequences and to make an alignment. It would be nice to be able to do that for both, DNA and protein.

The feature is implemented too. Thanks for your feedback

Great!

Looking forward for the next version.


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