tantan tutorial

2012-10-24

Installing tantan

Go to the tantan homepage:

http://www.cbrc.jp/tantan/

Download the latest version.

Open a terminal window:

green1.png

(Green on black: レトロ!)

Figure out where tantan was put (maybe "Downloads"?) and cd there.

If it is still zipped, unzip it:

$ unzip tantan-13.zip

Go into the tantan directory:

$ cd tantan-13

Compile it:

$ make

Finally, install it:

$ sudo make install

(The "sudo" requests administrator permission.)

Running tantan on DNA

Let's run tantan on the HOYA (ホヤ) mitochondrial genome. (HOYA is a very interesting animal.)

Download hoya-mito.fasta from here:

http://www.cbrc.jp/tantan/tutorial/files/

cd into the directory where it got saved (maybe "Downloads" again?) and run tantan like this:

$ tantan hoya-mito.fasta > out.fasta

Now look at the output file, out.fasta. You can view it with a web browser, or a text editor, or "less":

$ less out.fasta

In "less", use the arrow keys to move up and down, and type q to quit.

Running tantan on protein

Let's run tantan on huntingtin. Download it from here:

http://www.cbrc.jp/tantan/tutorial/files/

Run tantan with -p to tell it that the sequence is protein, not DNA:

$ tantan -p huntingtin.fasta > out2.fasta

Now look at the output.

Why are simple repeats in huntingtin interesting? (If you don't know, please search the Web.)