Assumptions This Book Makes

Assumptions This Book Makes

We assume that you have some familiarity with sequence analysis and its databases and tools, as well as basic working knowledge of your computer environment. For example, you understand how to install a program locally on your machine, and you know how to use command-line options in your tools and on your operating system.

We also assume that the information for each database or tool will not change significantly from the initial writing of the book.

Conventions Used in This Book

We use the following font conventions in this book:

Italic is used for:

  • Unix pathnames, filenames, and program names

  • Internet addresses, such as domain names and URLs

  • New terms where they are defined

Boldface is used for:

  • Names of GUI items: window names, buttons, menu choices, etc.

Constant Width is used for:

  • Command lines and options that should be typed verbatim

  • Names and keywords in Java programs, including method names, variable names, and class names

  • XML element tags

How to Contact Us

We have tested and verified the information in this book and in the source code to the best of our ability, but given the number of tools described in this book and the rapid pace of technological change, you may find that features have changed or that we have made mistakes. If so, please notify us by writing to:

O'Reilly & Associates
1005 Gravenstein Highway
Sebastopol, CA 95472
800-998-9938 (in the U.S. or Canada)
707-829-0515 (international or local)
707-829-0104 (fax)

To ask technical questions or comment on the book, send email to:

We have a web site for this book where you can find errata and other information about this book. You can access this page at:

For more information about this book and others, see the O'Reilly web site:


We would like to thank Reinhard Schneider and Friedrich von Bohlen at LION bioscience AG (Europe) and Mark Canales and Rudy Potenzone at LION bioscience Inc. (US) for fostering an environment of scientific and technical innovation. Thanks also to Hartmut Voss, Mike Dickson, and Beth Sump for their encouragement and support as we wrote this book. In addition, we would like to thank the past and present architects, developers, software QA members, technical writers, and our officemates at LION. They all asked good questions and made us better at what we do.

Thanks also to Georg Beckmann at Schering AG and Mark Graves at Berlex Laboratories for their real-world problems and our great discussions about how to solve them. We learned much from you.

A special thanks goes to our technical reviewers, Helge Weissig and Cynthia Gibas. Their insightful comments made us rethink the scope of the book and led us to make it more complete.

And finally, we want to thank Lorrie LeJeune, our editor, for planting the seed for this book and working with us on this fun project over the past few months. She made this whole process seem so painless that we're looking forward to working on another book with her. We also want express our gratitude to Philip Dangler, Todd Mezzulo, and the very professional staff at O'Reilly for turning our manuscript into a real book.

From Darryl

I'd like to thank my students, who inspired me to create a practical bioinformatics resource for use in classes and in research.

Susan S. Taylor at UCSD, Bettina Oelke at UCSC Extension, my best friend, Chris Soliz, and my loving parents and siblings have supported me both professionally and personally. My endless thanks go out to them. I'd also like to thank my coauthor, Scott, who listened to my suggestions and shared the desire to create a great book for our readers. I look forward to future collaborations with him.

Most of all, I want to thank my wife, Alison. As a writer herself, she shared my excitement as I finished this book, and understands how much it means to me. Every day we look forward to our future together.

From Scott

As a Christian I want to start by thanking God for His many blessings, including the opportunity to write this book.

Mick Noordewier gave me my first opportunity in bioinformatics when he offered me a job at the R. W. Johnson Pharmaceutical Research Institute (now Johnson & Johnson Pharmaceutical Research and Development). I learned a lot from Mick about the problems scientists really want to solve.

At NetGenics, Mike Dickson and Manuel Glynias believed in me and provided a wonderful environment in which to mix my scientific and software skills. I'll always be grateful.

I've profited greatly from my involvement with the Object Management Group's (OMG) Life Sciences Research (LSR) Domain Task Force. In particular, I'd like to acknowledge the co-submitters and evaluators of the Biomolecular Sequence Analysis specification from whom I learned so much.

Thanks to my parents, Wayne and Caryl Markel, who have always loved me and encouraged me, and showed me how important learning is.

Thanks also to my coauthor, Darryl, and to Alison for her encouragement. Darryl and I discovered a lot about each other and ourselves while writing this book.

My children—Klaudia, Nathan, and Victor—often remind me that there's more to life than work and writing a book. They continually let me re-experience the world through their eyes. I hope they always keep a portion of their childlike innocence.

And finally, my thanks and appreciation go to my wife Danette, the love of my life. Her encouragement, sound advice, and belief in me are truly amazing. Words can only begin to express what she means to me.