X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=86097eae50d6c0586d2c146c1608bc8d9a1e0260;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=09529a5ebb2cd532e4d0f77f24426a9c90f3ddd8;hpb=464c588a97e6bc11c5fb6b14e6764fbe997cb6b0;p=jalview.git diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 09529a5..86097ea 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,21 +1,24 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Principal Component Analysis @@ -31,12 +34,13 @@ for very large sets of sequences - usually because the JVM has run out of memory. A future release of Jalview will be able to avoid this by executing the calculation via a web service.

-

About PCAPrincipal components analysis is a technique for examining the +

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 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.

@@ -45,27 +49,32 @@ 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.

+

+ 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. The original method - preconditions the matrix by multiplying it with its transpose, and - this mode is enabled by unchecking the 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 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 @@ -105,5 +114,6 @@ 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.