[Jalview-discuss] Multiple sequence alignments with user defined anchor points

[Jim Procter]

  Hi Carlos, thanks for the email.

On 28/07/2010 22:35, Donado, Carlos A wrote:
> Is there any way to define anchor points before performing one of the MSA algorithms available in Jalview?
Currently, no - at least not in the way that you'd identify anchorpoints 
as a separate set of constraints to programs like Cobaln, DIALIGN or 
T-COFFEE. However, it would be possible in principle to use the column 
selection or groups in the current view to define the anchor 
points/fixed regions that should be constrained in the alignment, and 
I'd like Jalview to be able to do this in the future.

Having said this, its worth mentioning that Jalview does allow a kind of 
'poor man's' anchorpoint to be defined when aligning sequences. If you 
know a range of columns in a view are correctly aligned, then hide them, 
and then submit the view for alignment - they will be preserved in the 
result. If you take a look at exercise 20 in section 2.3.3 of the 
Jalview tutorial 
(http://www.jalview.org/tutorial/TheJalviewTutorial_screen.pdf), it 
explains how hidden regions are treated when the current view is sent to 
an alignment webservice.

Jim.


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