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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
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* Jalview is free software: you can redistribute it and/or
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<head>
<title>Principal Component Analysis</title>
</head>
of memory. A future release of Jalview will be able to avoid this by
executing the calculation via a web service.</p>
-<p><strong>About PCA</strong>Principal components analysis is a technique for examining the
+<p><strong>About PCA</strong></p>
+<p>Principal components analysis is a technique for examining the
structure of complex data sets. The components are a set of dimensions
-formed from the measured values in the data set, and the principle
+formed from the measured values in the data set, and the principal
component is the one with the greatest magnitude, or length. The sets of
measurements that differ the most should lie at either end of this
-principle axis, and the other axes correspond to less extreme patterns
+principal axis, and the other axes correspond to less extreme patterns
of variation in the data set.</p>
<p>
alignments. In both cases, components are generated by an eigenvector
decomposition of the matrix formed from the sum of substitution matrix
scores at each aligned position between each pair of sequences -
- computed either with <a href="scorematrices.html#blosum62">BLOSUM62</a> or the <a
- href="scorematrices.html#simplenucleotide">simple single nucleotide
- substitution matrix</a>. The options available for calculation are given
- in the <strong><em>Change Parameters</em></strong> menu.<br />
- Jalview allows two types of PCA calculation. The default <em><strong>Jalview
- PCA Calculation</strong></em> mode (indicated when that option is ticked in the <strong><em>Change
- Parameters</em></strong> menu) of the viewer performs PCA on a matrix where
- elements in the upper diagonal give the sum of scores for mutating in
- one direction, and the lower diagonal is the sum of scores for
- mutating in the other. For protein substitution models like BLOSUM62,
- this gives an asymmetric matrix, and a different PCA to one produced
- with the method described in the paper by G. Casari, C. Sander and A.
- Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
+ computed with one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>, <a
+ href="scorematrices.html#pam250">PAM250</a>, or the <a
+ href="scorematrices.html#simplenucleotide">simple single
+ nucleotide substitution matrix</a>. The options available for
+ calculation are given in the
+ <strong><em>Change Parameters</em></strong> menu.</p>
+ <p>
+ <em>PCA Calculation modes</em><br/>
+ The default Jalview calculation mode
+ (indicated when <em><strong>Jalview PCA Calculation</strong></em> is
+ ticked in the <strong><em>Change Parameters</em></strong> menu) is to
+ perform a PCA on a matrix where elements in the upper diagonal give
+ the sum of scores for mutating in one direction, and the lower
+ diagonal is the sum of scores for mutating in the other. For protein
+ substitution models like BLOSUM62, this gives an asymmetric matrix,
+ and a different PCA to a matrix produced with the method described in the
+ paper by G. Casari, C. Sander and A. Valencia. Structural Biology
+ volume 2, no. 2, February 1995 (<a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
- and implemented at the SeqSpace server at the EBI. The original method
- preconditions the matrix by multiplying it with its transpose, and
- this mode is enabled by unchecking the <strong><em>Jalview
+ and implemented at the SeqSpace server at the EBI. This method
+ preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
PCA Calculation</em></strong> option in the <strong><em>Change
Parameters</em></strong> menu.
</p>
-<img src="pcaviewer.gif">
+ <img src="pcaviewer.gif">
<p><strong>The PCA Viewer</strong></p>
<p>This is an interactive display of the sequences positioned within
the similarity space, as points in a rotateable 3D scatterplot. The
<p>
<em>The output of points and transformed point coordinates was added to the Jalview desktop in v2.7.</em>
<em>The Reset button and Change Parameters menu were added in Jalview 2.8.</em>
+<em>Support for PAM250 based PCA was added in Jalview 2.8.1.</em>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff