X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=b3d44dbf1c49e3c5623d1b4b5fc0f309ed568396;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=d97decab92d96695367006b8e401136104d237aa;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index d97deca..b3d44db 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,55 +1,137 @@ + +Clustal Colour Scheme + -

Clustal X Colour Scheme

-

This is an emulation of the default colourscheme used for alignments in - Clustal X, a graphical interface for the ClustalW multiple sequence alignment - program. Each residue in the alignment is assigned a colour if the - amino acid profile of the alignment at that position - meets some minimum criteria specific for the residue type.

-

The table below gives these criteria as clauses: {+X%,xx,y}, - where X is the minimum percentage presence for any of the xx (or y) residue types.

-
-

 

- - -
Clustal X Default Colouring
- - - - - - - - - - - - - - - -
Residue at positionApplied Colour{ Threshhold, Residue group }
A,I,L,M,F,W,VBLUE{+60%, WLVIMAFCHP}
R,KRED{+60%,KR},{+80%, K,R,Q}
NGREEN{+50%, N}, {+85%, N,Y}
CBLUE{+60%, WLVIMAFCHP}
CPINK{100%, C}
QGREEN{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}
EMAGENTA{+60%,KR},{+50%,QE},{+85%,E,Q,D}
DMAGENTA{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}
GORANGE{+0%, G}
H,YCYAN{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}
PYELLOW{+0%, P}
S,TGREEN{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}
-
-
+

+ Clustal X Colour Scheme +

+

This is an emulation of the default colourscheme used for + alignments in Clustal X, a graphical interface for the ClustalW + multiple sequence alignment program. Each residue in the alignment + is assigned a colour if the amino acid profile of the alignment at + that position meets some minimum criteria specific for the residue + type.

+

The table below gives these criteria as clauses: {>X%,xx,y}, + where X is the threshold percentage presence for any of the xx (or y) + residue types. +
For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).

+
+

 

+ + + + + + + +
Clustal X Default Colouring
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CategoryColourResidue at position{ Threshold, Residue group }
HydrophobicBLUEA,I,L,M,F,W,V{>60%, WLVIMAFCHP}
C{>60%, WLVIMAFCHP}
Positive chargeREDK,R{>60%,KR},{>80%, K,R,Q}
Negative chargeMAGENTAE{>60%,KR},{>50%,QE},{>85%,E,Q,D}
D{>60%,KR}, {>85%, K,R,Q}, {>50%,ED}
PolarGREENN{>50%, N}, {>85%, N,Y}
Q{>60%,KR},{>50%,QE},{>85%,Q,E,K,R}
S,T{>60%, WLVIMAFCHP}, {>50%, TS}, {>85%,S,T}
CysteinesPINKC{>85%, C}
GlycinesORANGEG{>0%, G}
ProlinesYELLOWP{>0%, P}
AromaticCYANH,Y{>60%, WLVIMAFCHP}, {>85%, + W,Y,A,C,P,Q,F,H,I,L,M,V}
UnconservedWHITEany / gapIf none of the above criteria are met
+