In this case, the components are generated by an eigenvector decomposition of the matrix formed from the sum of BLOSUM scores at each -aligned position between each pair of sequences. The basic method is -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.
@@ -43,19 +63,30 @@ View menu is checked, and the plot background colour changed from the View→Background Colour.. dialog box. The File menu allows the view to be saved (File→Save submenu) as an EPS or PNG image or printed, and the original alignment data and matrix resulting -from its PCA analysis to be retrieved. +from its PCA analysis to be retrieved. The coordinates for the whole PCA +space, or just the current view may also be exported as CSV files for +visualization in another program or further analysis.+
Options for coordinates export are:
+A tool tip gives the sequence ID corresponding to a point in the space, and clicking a point toggles the selection of the corresponding -sequence in the associated alignment window views. Rectangular region +sequence in the associated alignment window views. By default, points are only associated with the alignment view from which the PCA -was calculated, but this may be changed via the Associate +was calculated, but this may be changed via the View→Associate Nodes sub-menu.
Initially, the display shows the first three components of the similarity space, but any eigenvector can be used by changing the selected dimension for the x, y, or z axis through each ones menu -located below the 3d display.
+located below the 3d display. The Reset button will reset axis and rotation settings to their defaults. +
+The output of points and transformed point coordinates was added to the Jalview desktop in v2.7. +The Reset button, and Nucleotide or Protein calculation settings were added in Jalview 2.8.