Practical Bioinformatics

Practical Bioinformaticsis specifically designed for biology majors, with heavy emphasis on learning the steps necessary to perform bioinformatics analysis to answer biological questions. The chapters are focused on sequence analysis activities, a frequently performed subset of the field of bioinformatics. This book is written for courses that have a practical, hands-on element and contains many exercises (e.g. database searches, protein analysis, data interpretation) to complement the straightforward and practical topics. This book is focused on the analysis of DNA, RNA, and protein sequences. The chapters take the reader through a commonly asked question "what can I learn about this sequence?" This book is designed to be the student's first text for learning how to perform bioinformatics sequence analysis. There are many published books that teach about fascinating algorithms, sophisticated programs, and advanced interpretation of data. Although these are excellent sources of information, many readers are not prepared for, nor do they need, the depth and details of these texts. Although a thorough, conceptual background on each topic will be provided, the vast majority of the time spent with this book is on 'doing', not reading. By the time the student finishes the book, they will understand sequence analysis problems, approaches, and solutions so that they should be ready to perform many analysis steps on their own, and tackle more advanced books on the subject if needed or desired. Each chapter will briefly introduce concepts but quickly get to analysis problems using gene/protein examples that are specifically selected to demonstrate the concepts. Adequate background, details, illustrations, and references will be provided to ensure that students understand the fundamentals and can do further reading if desired. This text will emphasize the need to evaluate new tools as well as the proper use of established analysis software. There are literally hundreds of bioinformatics tools available and no book could possibly contain or instruct on all the tools that are available. However, the repeated experience of performing guided analysis problems will teach the reader to be critical of bioinformatics software and to use proper positive and negative controls when testing unfamiliar tools.