X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=0c39a15ba045ccba34e03db9fa646fad4fe95528;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=dd436c8d94ed52e9158da14ce01ab388e698edbc;hpb=51b6a83c3eb462f1a0cb76a8b4111521a4554fac;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index dd436c8..0c39a15 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,45 +1,125 @@ - -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 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}
+
+ +