<em>Calculating PCAs for aligned sequences</em><br />Jalview can
perform PCA analysis on both proteins and nucleotide sequence
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 with one of the available score
- matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the <a href="calculations.html">calculations dialog</a>, and
+ may use 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.
+ nucleotide substitution matrix</a>, or by sequence percentage identity,
+ or sequence feature similarity.
</p>
<img src="pcaviewer.gif">
<p>
and implemented at the SeqSpace server at the EBI. To reproduce
calculations performed with earlier Jalview releases it is necessary
to execute the following Groovy script:
-
<pre>
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+ jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
</pre>
- Additionally, for PCAs performed with older versions of Jalview and
- the Blosum62 matrix, it is also necessary to import the legacy
- BLOSUM62 score matrix (which is asymmetric for mutations between C to
- R) which can be downloaded at
- http://www.jalview.org/examples/legacyBlosum62.scm
+ This script enables the legacy PCA mode where gaps were treated as
+ 'X', and to modify the BLOSUM62 matrix so it is asymmetric for
+ mutations between C to R (this was a typo in the original Jalview
+ BLOSUM62 matrix which was fixed in 2.10.2).
</p>
-
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