X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=b3d44dbf1c49e3c5623d1b4b5fc0f309ed568396;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=7c5f7a8852b9d15eb9270872d80a72a1120ca847;hpb=8e55529daa9d811b947a0847969ba171fc26b690;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 7c5f7a8..b3d44db 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,21 +1,137 @@ - -Clustal Colour Scheme - - - - -

Clustal X

-

Clustal X is a graphical interface for the ClustalW multiple sequence alignment - program. Sequences can be coloured either by assigning a colour to specific - residues, or on the basis of an alignment consensus. The residues in each - column are coloured 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 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).

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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
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+ +