</head>
<body>
-<p> <em>Colouring above a percentage identity threshold</em></p>
+<p> <strong>Colouring above a percentage identity threshold</strong></p>
<p> Selecting this option causes the colour scheme to be applied to only those
residues that occur in that column more than a certain percentage of the time.
For instance selecting the threshold to be 100 will only colour those columns
<body>
-<p><em>Blosum62</a></em> </p>
+<p><strong>Blosum62</a></strong> </p>
<p>Gaps are coloured white. If a residue matches the consensus sequence residue
at that position it is coloured dark blue. If it does not match the consensus
residue but the 2 residues have a positive Blosum62 score, it is coloured light
</head>
<body>
-<p><em>Buried index</em></p>
+<p><strong>Buried index</strong></p>
<div align="center">
<table width="400" border="1">
<tr>
</head>
<body>
-<p><em>Clustal X Colour Scheme</em></p>
+<p><strong>Clustal X Colour Scheme</strong></p>
<p>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
-->
<head><title>Colouring by Conservation</title></head>
<body>
-<p><em>Colouring by Conservation</em></p>
+<p><strong>Colouring by Conservation</strong></p>
<p>This is an approach to alignment colouring which highlights
regions of an alignment where physicochemical properties are
conserved. It is based on the one used in
</head>
<body>
-<p><em>Helix Propensity</em> </p>
+<p><strong>Helix Propensity</strong> </p>
<div align="center">
<table width="400" border="1">
<tr>
</head>
<body>
-<p><em>Hydrophobicity</em></p>
+<p><strong>Hydrophobicity</strong></p>
<p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J.
Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this
table are coloured red and the most hydrophilic ones are coloured blue.</p>
</head>
<body>
-<p><em>Nucleotide Colours</em></p>
+<p><strong>Nucleotide Colours</strong></p>
<div align="center">
<table width="200" border="1">
<tr>
</head>
<body>
-<p><em>PID Colours</em><br>
+<p><strong>PID Colours</strong><br>
<br>
The PID option colours the residues (boxes and/or text) according to the percentage
of the residues in each column that agree with the consensus sequence. Only
</head>
<body>
-<p><em>Purine/Pyrimidine Colours</em></p>
+<p><strong>Purine/Pyrimidine Colours</strong></p>
<div align="center">
<table width="200" border="1">
<tr>
</head>
<body>
-<p><em>Strand propensity</em></p>
+<p><strong>Strand propensity</strong></p>
<div align="center">
<table width="400" border="1">
<tr>
</head>
<body>
-<p><em><a name="taylor">Taylor</a></em></p>
+<p><strong><a name="taylor">Taylor</a></strong></p>
<p>These colours were invented by Willie Taylor and an entertaining description
of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>
<div align="center">
</head>
<body>
-<p><em>Turn propensity</em></p>
+<p><strong>Turn propensity</strong></p>
<div align="center">
<table width="400" border="1">
<tr>
</head>
<body>
-<p><em>Zappo Colours</em><br>
+<p><strong>Zappo Colours</strong><br>
<br>
The residues are coloured according to their physicochemical properties as
follows: </p>