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> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 7, 2014, at 7:47 AM, Anton Feenstra <[email protected]> wrote: > Hi Jim, > > This is almost too trivial to ask, but can JalView calculate SP scores > (and similar alignment statistics)? There is an option 'Extract > scores...' in the Calculate menu, but that does not appear to do > anything when I use it. > > (I must admit I'm still on 2.8...) > > -- > Groetjes, > > Anton > _____________ _______________________________________________________ > | | | > | _ _ ___,| K. Anton Feenstra | > | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | > |( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands | > | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | > | | [email protected] - www.few.vu.nl/~feenstra/ | > | | "Move about like a Scientist, lay down, get kissed" | > | | (Red Hot Chili Peppars) | > |_____________|_______________________________________________________| > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
