Principal Component Analysis
-This is a method of clustering sequences based on the method developed by G.
- Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, February
- 1995 . Extra information can also be found at the SeqSpace server at the EBI.
-
- The version implemented here only looks at the clustering of whole sequences
- and not individual positions in the alignment to help identify functional residues.
- For large alignments plans are afoot to implement a web service to do this 'residue
- space' PCA remotely.
When the Principal component analysis option is selected all the sequences - ( or just the selected ones) are used in the calculation and for large numbers - of sequences this could take quite a time. When the calculation is finished - a new window is displayed showing the projections of the sequences along the - 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences cluster. -
-This 3d view can be rotated by holding the left mouse button down in the PCA - window and moving it. The user can also zoom in and out by using the up and - down arrow keys.
-Individual points can be selected using the mouse and selected sequences show - up green in the PCA window and the usual grey background/white text in the alignment - and tree windows.
-Different eigenvectors can be used to do the projection by changing the selected
- dimensions in the 3 menus underneath the 3d window.
-
+ Principal Component Analysis +
+A principal component analysis can be performed via the + calculations dialog which is accessed by selecting Calculate→Calculate + Tree or PCA....
+This calculation creates a spatial representation of the + similarities within a selected group, or all of the sequences in an + alignment. After the calculation finishes, a 3D viewer displays the + set of sequences as points in 'similarity space', and similar + sequences tend to lie near each other in the space.
+
+ Caveats
The calculation can be computationally
+ expensive, and may fail for very large sets of sequences - usually
+ because the JVM has run out of memory. However, the PCA
+ implementation in Jalview 2.10.2 employs more memory efficient
+ matrix storage structures, allowing larger PCAs to be performed.
+
+ About PCA +
+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 + 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 principal axis, and the other axes correspond to + less extreme patterns of variation in the data set.
+ +
+ Calculating PCAs for aligned sequences
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 BLOSUM62,
+ PAM250, or the simple single
+ nucleotide substitution matrix. The options available for
+ calculation are given in the Change
+ Parameters menu.
+
+ PCA Calculation modes
The default Jalview
+ calculation mode (indicated when Jalview
+ PCA Calculation is ticked in the Change
+ Parameters 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 (pubmed)
+ 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 Jalview
+ PCA Calculation option in the Change
+ Parameters menu.
+
+ + The PCA Viewer +
+This is an interactive display of the sequences positioned + within the similarity space, as points in a rotateable 3D + scatterplot. The colour of each sequence point is the same as the + sequence group colours, white if no colour has been defined for the + sequence, and green if the sequence is part of a the currently + selected group.
++ The 3d view can be rotated by dragging the mouse with the left + mouse button pressed. The view can also be zoomed in and out with + the up and down arrow keys (and the roll bar of the + mouse if present). Labels will be shown for each sequence if the + entry in the 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. 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. + + By default, points are only associated with the alignment view from + which the PCA 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. 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 Change Parameters menu were added in Jalview 2.8. Support + for PAM250 based PCA was added in Jalview 2.8.1. + +