<mapID target="colours.pid" url="html/colourSchemes/pid.html" />\r
<mapID target="colours.user" url="html/colourSchemes/user.html"/>\r
<mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>\r
- <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>\r
+ <mapID target="colours.conservation"\r
+ url="html/colourSchemes/conservation.html"/>\r
+\r
+ <mapID target="calcs.alquality"\r
+ url="html/calculations/quality.html"/> \r
+ <mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>\r
\r
<mapID target="menus" url="html/menus/index.html"/>\r
<mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>\r
<tocitem text="Sequence Feature Styles" target="seqfeatures"/>\r
</tocitem>\r
<tocitem text="Release History" target="release"/>\r
- <tocitem text="Alignment Annotations" target ="alannotation"/>\r
- \r
+ <tocitem text="Alignment Annotations" target ="alannotation" expand="false">\r
+ <tocitem text="Conservation" target="calcs.alconserv"/>\r
+ <tocitem text="Quality" target="calcs.alquality"/>\r
+ </tocitem>\r
<tocitem text="Input / Output" target="io"/>\r
<tocitem text="Key Strokes" target="keys"/>\r
<tocitem text="Making figures" target="export"/>\r
--- /dev/null
+<html>
+<head><title>Alignment Conservation Annotation</title></head>
+<body><p><strong>Alignment Conservation Annotation</strong></p>
+<p>This is an automatically calculated quantitative alignment
+annotation which measures the number of conserved physico-chemical
+properties conserved for each column of the alignment. Its calculation
+is based on the one used in
+ the AMAS method of multiple sequence alignment analysis :<br>
+<ul>Livingstone
+ C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
+ for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
+ No. 6 (745-756)).
+</ul>
+</p>
+<p>Conservation is measured as a numerical index reflecting the
+conservation of physico-chemical properties in the alignment:
+Identities score highest, and the next most conserved group contain
+substitutions to amino acids lying in the same physico-chemical
+class.</p>
+
+<p><em>Colouring an alignment by conservation</em><br>
+Conservation scores can be used to colour an alignment. This is
+explained further in the help page for <a
+href="../colourSchemes/conservation.html">conservation colouring</a>.
+</p>
+</body>
+</html>
--- /dev/null
+<html>\r
+<head><title>Alignment Quality Annotation</title></head>\r
+<body>\r
+<p><strong>Alignment Quality Annotation</strong></p>\r
+<p>Alignment Quality is one of the automatically calculated\r
+quantitative alignment\r
+annotations displayed below the columns of a multiple sequence\r
+alignment (and can be used to shade the alignment). It is an ad-hoc\r
+measure of the likelihood of observing the mutations (if any) in a\r
+particular column of the alignment.</p>\r
+<p>\r
+More precisely, the quality score is inversely proportional to the\r
+average cost of all pairs of mutations oberved in a particular column\r
+of the alignment - a high alignment quality score for a column would\r
+suggest that there are no mutations, or most mutations observed are\r
+favourable.\r
+</p>\r
+\r
+<p><em>The Algorithm</em><br>\r
+The quality score is calculated for each column in an alignment by\r
+summing, for all mutations, the ratio of the two BLOSUM 62 scores for\r
+a mutation pair and each residue's conservered BLOSUM62 score (which\r
+is higher). This valueis normalised for each column, and then plotted\r
+on a scale from 0 to 1.\r
+</p>\r
+<p>\r
+Multiple alignment algorithms using the BLOSUM 62 substition matrices\r
+should, in theory, maximise alignment quality for an un-gapped\r
+alignment, and locally maximise quality for gapped alignments.\r
+</p>\r
+</body>\r
+</html>\r
<html>\r
-<head><title>Conservation Calculation</title></head>\r
+<head><title>Colouring by Conservation</title></head>\r
<body>\r
<p><em>Colouring by Conservation</em></p>\r
-<p>This is an approach to alignment colouring based on the one used in\r
+<p>This is an approach to alignment colouring which highlights\r
+ regions of an alignment where physicochemical properties are\r
+ conserved. It is based on the one used in\r
the AMAS method of multiple sequence alignment analysis (Livingstone\r
C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9\r
- No. 6 (745-756)). \r
+ No. 6 (745-756)). See the <a href="../calculations/conservation.html">conservation calculation</a> help page for\r
+ a more thorough explanation of the calculation.\r
</p>\r
-<p>Conservation is measured as a numerical index reflecting the\r
- conservation of physico-chemical properties in the alignment:\r
- Identities score highest, and the next most conserved group contain\r
- substitutions to amino acids lying in the same physico-chemical\r
- class.</p>\r
<p>For an already coloured alignment, the conservation index at each\r
alignment position is used to modify the shading intensity of the\r
colour at that position. This means that the most conserved columns\r
in each group have the most intense colours, and the least conserved\r
are the palest. The slider controls the contrast between these\r
extremes.</p>\r
-<p>Conservation can be calculated over the whole alignment, or just\r
- within specific groups of sequences (such as those defined by\r
+<p>Conservation can be calculated over all sequences in an alignment, or just\r
+ within specific groups (such as those defined by\r
<a href="../calculations/tree.html">phylogenetic tree partitioning</a>).\r
The option 'apply to all groups' controls whether the contrast\r
slider value will be applied to the indices for the currently\r
git://source.jalview.org / jalview.git / commitdiff