X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=173728031cf7437d7be77e0bd7a1855c906eedb6;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=c15eda45e51e9fb031a92bda09d075f3ba22cd67;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index c15eda4..1737280 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,24 +1,63 @@ - -Clustal Colour Scheme - - - - -

Clustal X

-
-

Clustal X is a graphical interface for the ClustalW multiple sequence alignment - program. Sequences can be colored either by assigning a color to specific - residues, or on the basis of an alignment consensus. The residues in each - column are colored according to the consensus character assigned to that column. - In this way, you can choose to highlight, for example, conserved hydrophylic - or hydrophobic positions in the alignment.

-

-
- - + + +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}
+
+
+ +