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Molecular phylogenetic tree.

In this section you will plot a dendrogram displaying the measured similarities between the seven proteins which you pairwise aligned in Section 5. You will compare there relative position in the dendrogram to their relative position in the phylogenetic tree of life.

Below is the pairwise alignment scores from the 21 pairs aligned in section 5. The information in ~/tbss.work/Bioinformatics/multipleData/stats is assembled into a symmetric matrix:


  1EQR 1ATI 1ADJ 1EFW 1ASZ 1B8A 1BBW
1EQR 0.0 0.21 0.23 0.55 0.28 0.31 0.31
1ATI 0.21 0.0 0.25 0.24 0.24 0.18 0.21
1ADJ 0.23 0.25 0.0 0.24 0.24 0.21 0.23
1EFW 0.55 0.24 0.24 0.0 0.34 0.36 0.30
1ASZ 0.28 0.24 0.24 0.34 0.0 0.41 0.27
1B8A 0.31 0.18 0.21 0.36 0.41 0.0 0.28
1BBW 0.31 0.21 0.23 0.30 0.27 0.28 0.0

The commands in the following Matlab session are all in the Matlab script Dendro.m. The commands can be run all at once simply by typing Dendro at the Matlab command line when Matlab's current directory contains Dendro.m.

Now we will use the clustering algorithms in the Statistics toolbox of Matlab to draw a dendrogram of the relatedness of the domains. Here we use the above scores derived from sequence alignment, but structure alignment scores could be used as well[4].

\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...hat we know about the evolution of the three domains of life?}
\end{minipage} }

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