Dear Jalview team,
May I suggest that there is a small bug in the Clustalx colouring scheeme, - and, if I’m not wrong, it comes from the original Clustalx team (as I know it was there when they made it, - and I corrected my own coding scheeme for my running version). Anyway, - it is as follows:
In columns with conserved (major) Asp (D), Glu’s doesn’t get coloured (which they should; negatives!). The reverse situation is ok (i.e. D’s in columns with conserved/major E’s DO get coloured.
I include a snapshot from my alignment at hand, - but you really don’t need any sample, as any D/E-rich alignment with reveal this.
Cheers
Rein
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Rein Aasland, professor ! Tlf.: +47 555 845 31 (lab)
Department of Molecular Biology & ! +47 924 25 456 (mobil)
Computational Biology Unit, BCCS ! Fax.: +47 555 896 83
University of Bergen ! E-mail: aasland@mbi.uib.no
Thormoehlensgt 55 ! WWW: http://www.uib.no/rg/genreg
N-5020 Bergen, Norway ! WWW: http://www.cbu.uib.no/
p.t. on sabbatical leave to NIMR/MRC, Mill Hill, London