A Brief Bioinformatics Tutorial

What Is This About?

This is about how to use a computer to find what is known about a gene of interest and also how to get new insights about it.

The tutorial is divided in three main parts:

• In the Sequence part, you will see how to look efficiently for a particular protein sequence, how to blast it against the database of your choice to find homologues, how to perform a multiple alignment of the homologues you've selected and how to edit this alignment.
• The Structure part is about molecular visualization, homology modeling and structural domain prediction.
• In the Function part, you will be introduced to you 3 useful servers to investigate the function of a protein. i.e. finding interactors, co-expressed genes, see a phylogenetic profile, easily access papers citing your gene etc ...

During all the three parts, we will use the S. cerevisiae VPS36 protein as an example.

During the tutorial, you will click on links referring to a web-server to use. If you are using firefox or Opera, you can right click or Ctrl click and open the link in a TAB. In this way, you'll keep track of the tutorial and you won't end up with 10 windows.

Why Did I Choose These Programs?

Everything that you will use here has been chosen based on 4 criteria. (i) the program must run on a Mac with OS X, (ii) the program must be free, (iii) the program must be easy to handle. (iv) the program must be useful.

What If I Want To Learn More?

In general, all the tools used here have extensive help pages and tutorials. There are also mailing lists (here I'm thinking about Pymol in particular) where you can ask a question to thousands of experienced users at once! (try to read the manual first though).

There is a topic that is not discussed here because of time constraints but if (by any chance) you thought about starting programming, I strongly recommend the R language. It is easy to install and handle. Even with no prior knowledge about programming, you could handle it after a few days and make very nice pictures . If you heard about it, it is very similar to Matlab except it is free. Importantly, the R language was first written for statistics so you can easily perform any kind of statistical test with it.

What If I Have Questions Regarding This Tutorial?

I would first say that if you have a look at the documentation you will probably find an answer. However, if you cannot manage to find an answer there, then, if it is about Pymol you can ask Roger (rlw -at- mrc-lmb.cam.ac.uk). If it is about anything else you can ask Emmanuel (elevy -at- mrc-lmb.cam.ac.uk).