[Jalview-discuss] PCA

Jim Procter jprocter at compbio.dundee.ac.uk
Sat Jan 26 15:49:18 GMT 2013


oops - looks like I'd got some xtra text there:

On Sat Jan 26 15:45:16 2013, Jim Procter wrote:
> It sounds like you are asking about projecting sequences onto the PCA
> model in order to assess how they fit, which would be analogous to a
> common use for ordination based models where new observations are
> evaluated to see how well they fit some existing model.

sorry 'bout that. Also - you might want to check out JDet (at 
http://csbg.cnb.csic.es/JDet/ and https://code.google.com/p/jdet/) - 
since that also allows a residue level PCA to be performed on an 
alignment.. I'd be quite tempted to incorporate JDet's analysis and 
visualization components in Jalview, in fact.

Jim




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