From 2ff5639e0ba863bf19212971977524f0a3c955be Mon Sep 17 00:00:00 2001
From: Jim Procter
Date: Tue, 3 Jun 2014 14:26:22 +0100
Subject: [PATCH] JAL-1503 document updated PCA interface
---
help/html/calculations/pca.html | 38 ++++++++++++++++++++--------------
help/html/calculations/pcaviewer.gif | Bin 15569 -> 27629 bytes
2 files changed, 22 insertions(+), 16 deletions(-)
diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 0d6e85e..49019a7 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -46,25 +46,30 @@ of variation in the data set.
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 BLOSUM62 or the simple single nucleotide
- substitution matrix. The options available for calculation are given
- in the Change Parameters menu.
- Jalview allows two types of PCA calculation. The default Jalview
- PCA Calculation mode (indicated when that option is ticked in the Change
- Parameters 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 (BLOSUM62, PAM250, or the simple single
+ nucleotide substitution matrix. The options available for
+ calculation are given in the
+ Change Parameters menu.
Jalview allows
+ two types of PCA calculation. The default
+ Jalview PCA Calculation mode (indicated when
+ that option is ticked in the
+ Change Parameters 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 (pubmed)
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 Jalview
- PCA Calculation option in the Change
- Parameters menu.
+ this mode is enabled by unchecking the
+ Jalview PCA Calculation option in the
+ Change Parameters menu.
The PCA Viewer
@@ -106,5 +111,6 @@ located below the 3d display. The Reset button will re
The output of points and transformed point coordinates was added to the Jalview desktop in v2.7.
The Reset button and Change Parameters menu were added in Jalview 2.8.
+Support for PAM250 based PCA was added in Jalview 2.8.1.