luca.jovine at ki.se
Fri Nov 19 04:22:50 PST 2010
> Yes, and the target sequence (i.e. the protein that you crystallized) needs to be first. One annoying thing about MUSCLE is that it sorts sequences and (currently) won't let you disable this behavior, so you may need to do some cut-and-pasting. Maybe we need to modify the Python wrapper to do this automatically. (Although I think it would be even easier if Sculptor did the alignment automatically.)
This is actually a bit odd, since one could run version 3.7 of MUSCLE with a -stable flag that would output sequences in the the same order as the input... but apparently this has been disabled in the version that ships with PHENIX (3.8.31). Maybe we could just ask Robert Edgar to put it back?
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