Heya, I've recently switched from AliView to UGene. One of the features that I greatly miss is being able to make a selection of bases and clearing them, i.e., not filling the selection with GAPS but replacing/changing all nucleotides in the selection with GAPS.

Currently as part of my work, I need to replace my flank ends of transposable elements in the consensus sequence (which is added to the fasta file) to be used with RepeatModeller.

Right now, what I have to do is make a selection, delete it and then use the fill selection with gaps to replicate this functionality. I would greatly appreciate if this simple feature was added as it would be easier to track what I've modified for my consensus.

Thank you!

Hello,

The feature you are asking about is implemented already in some way. To use it:
1. Select the subsequence you want to replace.
2. Click the right mouse button, then find "Edit" -> "Replace subsequence" (or, simply click "Ctrl+R").
The selected subsequence will appear it the dialog. Make any changes and click "OK".

Best regards,
Dmitrii SUkhomlinov,
The UGENE team.

Thank you for your quick reply!

I'm not sure that Ctrl + R does anything on my version of UGENE (Ver 41.0), but I don't see this in the edit menu in the MSA viewer either.

I should also probably clarify further, that I don't want to modify individual bases but instead hopefully make it possible to make a selection of multiple bases and 'clearing' them instead of having to:

Edit -> Remove Selection
Edit -> Fill selection with gaps

The issue with "Fill selection with gaps" is that it shifts the sequence to the right when filled, and so requires you to first delete the selection and then fill it. It would be really nice to just be able to turn my selection into "-" instead of performing two steps.

In AliView, you can select multiple bases and clear them; basically changing that selection into ("-").