Multiple sequence alignments with user defined anchor points

Hi,

Is there any way to define anchor points before performing one of the MSA algorithms available in Jalview?

Thanks
Carlos

Hi Carlos, thanks for the email.

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.

ยทยทยท

On 28/07/2010 22:35, Donado, Carlos A wrote:

--
-------------------------------------------------------------------
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.