[Jalview-discuss] [Fwd: How do I open a gap in a large MSA and paste in a sequence block from another alignment?]

[James Procter]

Hi Carville.

Well done for finding my email address - although you should have been 
able to post this to jalview-discuss at jalview.org - maybe you need to 
register your new email ?



Carville G. Bevans III, Ph.D. wrote:
> Here's an /urgent/ "power user" question:
> 
> I have a large 327-sequence MSA (~160 residue protein domain) I created 
> in Jalview.  I made a copy of the .jar file and edited it to end up with 
> a 25 residue subsequence MSA for which I then opimized the alignment 
> separately.  Now I would like to paste the entire 327x25 subsequence MSA 
> back into the original large MSA, hopefully in one action.  (It would 
> take forever to use the sequence edit commands to do this one line at a 
> time!)
I agree. It would take forever. I take it that you used another program 
to do the optimisation ?   (read on below)
> Since I'm able to select whole verticle blocks of the MSA to work on, I 
> assume there must be some straightforward way of doing the cut-and-paste 
> I need.
Unfortunately, there isn't at the moment. I've planned to implementa not 
a 'copy subalignment' command for some time, and some of the code is 
already present as part of the alignment web service handler - but I 
haven't, as yet, made a general copy/paste type function.

Following on from my remark above: If you are happy with using one of 
the three alignment web services to refine the 25 residue MSA, then the 
quickest way to do this is to perform the optimisation again :
  1. Select one or more sets of contigous columns of the alignment that 
you want to optimize.
  2. Use the 'Select->Invert Column Selection' function (or 
shift+ctrl+I) followed by the 'View->Hide->Selected columns' function 
(or press H) to hide the parts of the alignment that you want to preserve.
  3. Select all the visible regions and submit them to the alignment 
service (note - don't use 'Clustal realign' - it won't do anything in 
this case). The web service job window will contain one alignment job 
for each contiguous region.
  4. Once all the jobs finish, you'll have a new alignment window 
containing the re-aligned blocks pasted together. The regions that you 
excluded from the optimisation process will still be hidden, so select 
'Reveal all hidden columns' to recover them.

However - if you've used something else to optimise the sub-alignment, 
the only thing I can suggest is to export both alignments in BLC format, 
  which is unique in that each aligned column is written as a row in the 
ASCII file. You'll then have to manually copy the lines from the 
optimised sub-alignment rows into the correct position in the original 
alignment, and delete the rows they replace.

I hope this helps.
Jim.

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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