X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=b3d44dbf1c49e3c5623d1b4b5fc0f309ed568396;hb=f2450b343be28d1b46f71a809d3d85041bf5aa62;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 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 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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