On Nov 9, 2014, at 8:17 AM, Anton Feenstra <[email protected]> wrote:
> On 08-11-14 23:38, Elaine Meng wrote: >> Hi Anton, >> Pardon me if I’m duplicating a previous answer, but I didn’t see one… >> >> There are various scores available via the AACon web service connected to >> Jalview as described here: >> <http://www.jalview.org/help/html/webServices/AACon.html> >> >> The Valdar paper cited in that page describes the options in more detail. >> Some of the scores are SP or very SP-like. I don’t recall seeing >> sub-options in the AACon dialog, so for some of these it may not be obvious >> which substituation matrix is used. The Valdar paper is here: >> <http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/full> >> >> Since I’m a Chimera person, I’ll also plug that program (very briefly, I >> know this is the JalView list!). Chimera can calculate sum-of-pairs >> conservation via the embedded AL2CO method, and you have your choice of a >> dozen or so different substitution matrices and what proportion of gaps are >> tolerated in a column. It can’t handle as large alignments as JalView can, >> however. The conservation values are easily/automatically mapped to any >> structures associated with the alignment. Tutorial example: >> <http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1> > > Thanks, I'll look into that! > > Jim, I basically need some scoring to compare alignments produced by > different tools/settings. Preferably, I'd use several scores so as not > to be dependent on one. Initially, it is just for students in a > practical, (starting tomorrow), but it is also a recurring use case for > my own research. Directing them to a webserver or even the jalview > console would work fine for this purpose. > > Pretty as JalView is, sometimes you just don't want to visually compare > all alternative alignments you may have for a particular dataset ;-O > Hi Anton, The AACon scores I mentioned before show up directly in the JalView window, below the sequence alignment. You call that calculation directly from the JalView menu; it’s all connected: <http://www.jalview.org/help/html/webServices/AACon.html> I also forgot to mention before that the JalView alignment quality score that also shows up below the alignment automatically (you don’t need to call AACon) is also very similar to an SP score, as described in the JalView manual: <http://www.jalview.org/help/html/calculations/quality.html> Best, Elaine _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
