Bioinformatics and Homology Modeling:
A Student-Tested Tutorial for Beginners

Exploring Human Visual Pigments

Bioinformatics Home Pages


This tutorial allows you to explore opsins -- the proteins that catch light for our eyes -- and the genes that code for opsins. But the real subject of this exercise is bioinformatics -- the use of computers to search for, explore, and use information about genes, nucleic acids, and proteins. While learning about the human opsins, you will use some of today's most powerful bioinformatics tools, and you will even build a model of a protein whose detailed structure is unknown (called homology modeling). You can follow up this tutorial with a study of opsins from other organisms, or by exploring any class of biomolecules that interest you.

Please realize that this tutorial merely scratches the surface of what you need to know in order to use bioinformatics wisely in your research. If you want to learn more, including vital guidance in judging the quality of your results, I recommend you turn next to Bioinformatics for Dummies, by Claverie and Notredame, Wiley Publishing, Inc., 2007.

I assume that you are conversant with biochemistry and molecular biology. If you see unfamiliar terms pertaining to the genes, mRNAs, and proteins used as examples here, break out your biochemistry text, head for the index, and review, review, review.

For more information about each database or tool, go to its home page and read, read, read. These tools come with plenty of help.


This web page was originally composed of somewhat sketchy procedures that I devised by playing* with bioinformatics tools on the web. For five years or so, my biochemistry students carried out the tutorial, and their suggestions led to many improvements, as have emails from users around the world.

*My play with bioinformatics tools started with the book Bioinformatics for Dummies, by Claverie and Notredame, Wiley Publishing, Inc., 2003. Not considering myself a dummie in most of my areas of interest, I had never looked very hard at Wiley's "Dummies" books. I'm so glad I looked at this one. The authors are on the frontiers of the field, and they have produced a serious, high quality book. If you want to work through lots of clear tutorials in all areas of bioinformatics, buy it. It was the best $30 I had spent on a book in quite a few years. Just click the title above to learn more about the latest edition, 2007 (only $20 now), which guided my October 2008 revisions of this tutorial.

Many thanks to Professors Claverie and Notredame for this friendly and powerful resource.