TP bioinformatique

Exercise : Analysis of synonymous and non-synonymous substitutions

1- Analysis of Ka and Ks in the Odysseus gene of different drosophila species:

	Ting CT, Tsaur SC, Wu ML, Wu CI.
	A rapidly evolving homeobox at the site of a hybrid sterility gene. Science. 1998 Nov 20;282(5393):1501-4. (PDF)

The alignement of coding regions of the Odysseus gene from D. melanogaster, D. sechellia, D. simulans and D. mauritiana is available here.

Compute the phylogenetic trees with Ka and then with Ks (use phylojava). Compare branch lengths in the Ka and Ks trees (compute the ratio Ka/Ks for each branch).

2- We will use the PAML package.

odysseus1.phy

odysseus.tree

odysseus1.ctl

Step 1: Install PAML on your computer

- download paml3.13d.tar.gz from the PAML site.

- uncompress this archive:
gzip -d paml3.13d.tar.gz

- un-tar this archive:
tar xvf paml3.13d.tar

- go to the repertory containing the source files:
cd paml3.13d/src

    - compile PAML:
        make -f Makefile.UNIX

    - move the executables to your bin repertory
        mv codeml ~/bin/
        mv baseml ~/bin/

NB: if this "bin" repertory does not exist, first create it:
mkdir ~/bin/

Step 2: Analyze the Ka/Ks (DN/dS) ratio in primates.

download the following files:

sequence alignment: lysozymeSmall.txt

phylogenetic tree: lysozymeSmall.trees

control file: lysozymeSmall.ctl

Run codeml:

codeml lysozymeSmall.ctl

For more training, look at the examples:

cd ~/paml3.13d/examples

Index

For review, see:

	Hurst LD.	Related Articles, Links
	The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002 Sep;18(9):486.