Trouble adding gaps to a group of sequences

Hi,
I have just started using Jalview, so this may be a simple question, but I am not sure how to solve it. I would like to add gaps to a group of sequences in an alignment, but I am having trouble doing so. I have Jalview installed (I am not using the webstart version) on a Mac running OS X 10.5.8. I am able to add gaps to one sequence using the left mouse button and the shift key, but when I hold down the apple key (command key) and try to drag my sequences using the left mouse button it does not add gaps. I have also tried the control key and the option key, but neither of these work. When I hold down the apple key it is almost as if the program thinks that I am right clicking on the selection, because when I hold down the command key and try to drag my sequences I get the selection menu and I am given the "Edit", "Output to text", "Group" etc options. I assume I am doing something wrong, but I am not sure what it is.

Any advice would be very much appreciated.

Thanks so much for your time,
Felicia

···

---------------------------------------------------------------
Felicia Gomez
Tishkoff Lab
Department of Genetics
University of Pennsylvania
430 Clinical Research Building
415 Curie Boulevard
fgomez@mail.med.upenn.edu
Lab Phone: 215-746-2683

The control key + dragging within a selected group of sequences will insert gaps into all the selected sequences. In the current version of Jalview, you have to select sequences before you can insert gaps into a group of them - I suspect you may not have done this. Try selecting a few sequences and then inserting gaps.

We plan to review the way that interactive editing works in Jalview - thanks for highlighting this minor (but significant) issue !

Thanks
Jim.

···

On 17/03/2010 21:53, Felicia Gomez wrote:

Hi,
I have just started using Jalview, so this may be a simple question,
but I am not sure how to solve it. I would like to add gaps to a
group of sequences in an alignment, but I am having trouble doing
so. I have Jalview installed (I am not using the webstart version)
on a Mac running OS X 10.5.8. I am able to add gaps to one sequence
using the left mouse button and the shift key, but when I hold
down the apple key (command key) and try to drag my sequences using
the left mouse button it does not add gaps.

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Hi again, Felicia.

Thanks so much for getting back to me! It is really appreciated when minor inquires like this get address. I'm sorry to quibble, but I have selected the region where I want to add the gap. To select a region I used my left mouse button and dragged the mouse to the bottom right corner of the region that I want (as it says in the manual). And I do get the dashed red box around the region I have selected. However, when I press the apple key (not control) I get the Selection option - as if I have right clicked. I know this is a minor issue and does not detract from the all that Jalview can do, but I thought I should be clear. Maybe it is a bug with the OS I am using? Or maybe it is just my machine....

no - its not your machine, its Jalview :slight_smile:

What is happening is that Jalview isn't letting you insert gaps because you've selected a region within the alignment. When only a small section of the alignment is selected, the 'locked editing' function comes in to play - so you first need to add in some gaps so you have room to maneouver within the locked region. However, Jalview doesn't give you any feedback to indicate that this is what is stopping you editing the alignment.. so it feels like something is broken.

Instead of selecting the small region of the alignment, click on the seuqence IDs to select the whole row for each sequence you want to edit. Then, you should be able to freely insert gaps using CTRL+click + drag.

Hope this helps!
Jim.

···

Thanks,
Felicia
---------------------------------------------------------------
Felicia Gomez
Tishkoff Lab
Department of Genetics
University of Pennsylvania
430 Clinical Research Building
415 Curie Boulevard
fgomez@mail.med.upenn.edu
Lab Phone: 215-746-2683

On Mar 18, 2010, at 7:22 AM, Jim Procter wrote:

On 17/03/2010 21:53, Felicia Gomez wrote:

Hi,
I have just started using Jalview, so this may be a simple question,
but I am not sure how to solve it. I would like to add gaps to a
group of sequences in an alignment, but I am having trouble doing
so. I have Jalview installed (I am not using the webstart version)
on a Mac running OS X 10.5.8. I am able to add gaps to one sequence
using the left mouse button and the shift key, but when I hold
down the apple key (command key) and try to drag my sequences using
the left mouse button it does not add gaps.

The control key + dragging within a selected group of sequences will
insert gaps into all the selected sequences. In the current version of
Jalview, you have to select sequences before you can insert gaps into a
group of them - I suspect you may not have done this. Try selecting a
few sequences and then inserting gaps.

We plan to review the way that interactive editing works in Jalview -
thanks for highlighting this minor (but significant) issue !

Thanks
Jim.

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.