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 -- 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
