Bioinformatics For Dummies

Jean-Michel Claverie, Cedric Notredame

• Publisher: For Dummies
• Year: 2011
• ISBN:
  9781118051108
• Edition: 2
• Topic: Biological Sciences
• Subtopic: Biotechnology
• Index: Biological Sciences

Were you always curious about biology but were afraid to sit through long hours of dense reading? Did you like the subject when you were in high school but had other plans after you graduated? Now you can explore the human genome and analyze DNA without ever leaving your desktop!

Bioinformatics For Dummies is packed with valuable information that introduces you to this exciting new discipline. This easy-to-follow guide leads you step by step through every bioinformatics task that can be done over the Internet. Forget long equations, computer-geek gibberish, and installing bulky programs that slow down your computer. You'll be amazed at all the things you can accomplish just by logging on and following these trusty directions. You get the tools you need to:

• Analyze all types of sequences
• Use all types of databases
• Work with DNA and protein sequences
• Conduct similarity searches
• Build a multiple sequence alignment
• Edit and publish alignments
• Visualize protein 3-D structures
• Construct phylogenetic trees

This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes. It provides tips for using servers and places to seek resources to find out about what's going on in the bioinformatics world. Bioinformatics For Dummies will show you how to get the most out of your PC and the right Web tools so you'll be searching databases and analyzing sequences like a pro!

Part I

Getting Started in Bioinformatics

In this part . . .

Bioinformatics is a new discipline, which means that nobody should feel ashamed if he or she doesn’t have a clue what the excitement’s all about. Don’t worry; after finishing this book, you’ll be speaking bioinformaticsspeak with the best of them.

We start you off in Part I with a quick reminder of what you need to know about DNA and proteins to make sense of this book. We also give you an overview of the main bioinformatics tools available on the Internet.

We don’t give too many details here, but if all you need to know is which Internet page to open and which button to press, come on in, ’cuz we’ve got just what you need!

Chapter 1

Finding Out What Bioinformatics Can Do for You

In This Chapter

Defining bioinformatics

Understanding the links between modern biology, genomics, and bioinformatics

Determining which biological questions bioinformatics can help you answer quickly

Organic chemistry is the chemistry of carbon compounds. Biochemistry is the study of carbon compounds that crawl.

— Mike Adam

It looks like biologists are colonizing the dictionary with all these bio-words: we have bio-chemistry, bio-metrics, bio-physics, bio-technology, bio-hazards, and even bio-terrorism. Now what’s up with the new entry in the bio-sweepstakes, bio-informatics?

What Is Bioinformatics?

In today’s world, computers are as likely to be used by biologists as by any other highly trained professionals — bankers or flight controllers, for example. Many of the tasks performed by such professionals are common to most of us: We all tend to write lots of memos and send lots of e-mails; many of us use spreadsheets, and we all store immense amounts of never-to-be-seen-again data in complicated file systems.

However, besides these general tasks, biologists also use computers to address problems that are very specific to biologists, which are of no interest to bankers or flight controllers. These specialized tasks, taken together, make up the field of bioinformatics. More specifically, we can define bioinformatics as the computational branch of molecular biology.

Time for a little bit of history. Before the era of bioinformatics, only two ways of performing biological experiments were available: within a living organism (so-called in vivo) or in an artificial environment (so-called in vitro, from the Latin in glass). Taking the analogy further, we can say that bioinformatics is in fact in silico biology, from the silicon chips on which microprocessors are built.

This new way of doing biology has certainly become very trendy, but don’t think that “trendy” translates into “lightweight” or “flash-in-the-pan.” Bioinformatics goes way beyond trendy — it’s at the center of the most recent developments in biology, such as the deciphering of the human genome (another buzzword), “system biology” (trying to look at the global picture), new biotechnologies, new legal and forensic techniques, as well as the personalized medicine of the future.

Because of the centrality of bioinformatics to cutting-edge developments in molecular biology, people from many different fields have been stumbling across the term in a variety of different contexts. If you’re a biology, medical, or computer science student, a professional in the pharmaceutical industry, a lawyer or a policeman worrying about DNA testing, a consumer concerned about GMOs (Genetically Modified Organisms), or even a NASDAQ investor interested in start-up companies, you’ll already have come across the word bioinformatics. If you’re good at what you do, you’ll want to know what all the fuss is about. This chapter, then, is for you.

Instead of a formal definition that would take hours to cover all the ins and outs of the topic, the best way to get a quick feel for what bioinformatics — or swimming, for that matter — is all about is to jump right into the water; that’s what we do next. Go ahead and get your feet wet with some basic molecular biology concepts — and the relevant questions intimately connected with such concepts — that all together define bioinformatics.

Analyzing Protein Sequences

If you eat steak, you’re intimately acquainted with proteins. (Your taste buds know them intimately anyway, even if your rational mind was too busy with dinner to master the concept.) For you non-steak lovers out there, you’ll be pleased to know that proteins abound in fish and vegetables, too. Moreover, all these proteins are made up of the same basic building blocks, called amino acids. Amino acids are already quite complex organic molecules, made of carbon, hydrogen, oxygen, nitrogen, and sulfur atoms. So the overall recipe for a protein (the one your r...