X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=195171eecde4d5db845e10244dde9cadde2e2a67;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=488f7451f6714eb5196ddeeaaeb85f6ef344403a;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 488f745..195171e 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,52 +1,65 @@ - - - - - - -

Clustal X

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NGPBD
SCYKX
QWTRH
ZEAFM
LVI
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- - + + +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.

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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.

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Clustal X Default Colouring
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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}
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