a small bug in ClustalX colouring scheeme

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.





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

Dear Rein.

I had noticed this behaviour myself, but when I compared it to ClustalX’s default, I saw the same behaviour and assumed it was simply a minor quirk of the default ruleset. Its clearly inconsistent, so I’ll add this to my list of minor bugs to fix.


J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
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