Computational Biology

A Hypertextbook

Scott T. Kelley, Dennis Didulo

• Publisher: ASM Press
• Year: 2018
• Print ISBN: 9781683670025
• eBook ISBN: 9781683673033
• Edition: 1
• Topic: Education
• Subtopic: Teaching Science & Technology

This textbook is for anyone who needs to learn the basics of bioinformatics—the use of computational methods to better understand biological systems. Computational Biology covers the principles and applications of the computational methods used to study DNA, RNA, and proteins, including using biological databases such as NCBI and UniProt; performing BLAST, sequence alignments, and structural predictions; and creating phylogenetic trees. It includes a primer that can be used as a jumping off point for learning computer programming for bioinformatics.

This text can be used as a self-study guide, as a course focused on computational methods in biology/bioinformatics, or to supplement general courses that touch on topics included within the book. Computational Biology's robust interactive online components "gamify" the study of bioinformatics, allowing the reader to practice randomly generated problems on their own time to build confidence and skill and gain practical real-world experience. The online component also assures that the content being taught is up to date and accurately reflects the ever-changing landscape of bioinformatics web-based programs.

CHAPTER

-1

GETTING STARTED

Using the Website

Direct your browser on your phone, computer, or tablet to the following website:

http://www.kelleybioinfo.org

There you will see the homepage, as shown at right.

Touching or clicking an icon (e.g., “Alignment”) will take you to a new page that has tools related to the icon topic. The Alignment, Motifs, and Phylogeny buttons teach algorithms and tools for many types of sequence analysis with DNA, RNA, and proteins. The Protein and RNA buttons focus on algorithms for predicting structural features of the functional macromolecules, while the Probability button teaches how to generate substitution matrices.

Example: The Alignment Page

Clicking or touching the Alignment button will take you to the following page, which begins with the BLAST algorithm interactive tool. All the pages use this basic design.

General features

Information on the interactive learning tool

Tutorials and test data for online bioinformatics software

While most of the pages look like the Alignment page, the Basics page is organized differently and mostly contains information and tutorials.

How To Use This Book

I will assume you are familiar with how to read/use a book, but remember that the physical book is meant to be used in conjunction with the online component. Throughout the text you will be directed to online modules via URLs and QR codes. The online material is not supplemental, but is a critical portion of this hypertextbook.

CHAPTER

00

INTRODUCTION

The word bioinformatics refers to the computational analysis of complex biological data. The “bio-” prefix indicates biology, of course, while “informatics” is the science of data processing, storage, and retrieval (a.k.a. information science) that first developed in the 1960s. Bioinformatics itself dates back to the early 1970s, when computers were first used to analyze molecular sequences. While our knowledge of biological processes, the amount of molecular data, and the speed and throughput of computation have all expanded dramatically, the field of bioinformatics still primarily focuses on the analysis of three critical biological molecules: DNA, RNA, and protein.

These molecules are critical to the cellular processes of all living organisms, and the analysis of the composition and patterns of these molecules should in theory reveal all the secrets to life. (Or, as Dr. Frankenstein would say, “It’s alive! Bwahaha!”) In fact, because DNA encodes the information for all the RNA and protein in every cell, analysis of DNA sequence patterns comprises the majority of bioinformatics. RNA and protein sequences are also analyzed using specific bioinformatics algorithms, but the sequences of these molecules are often computationally determined from the DNA sequence in one way or another (see below).

The purpose of this chapter is to explain the general properties of these biological molecules and ho...

Table of contents

• Cover
• Title Page
• Copyright
• Dedication
• Contents
• Preface
• For the Instructor
• For the Student
• Acknowledgments
• About the Authors
• Chapter –1. Getting Started
• Chapter 00. Introduction
• Chapter 01. BLAST
• Chapter 02. Protein Analysis
• Chapter 03. Sequence Alignment
• Chapter 04. Patterns in the Data
• Chapter 05. RNA Structure Prediction
• Chapter 06. Phylogenetics
• Chapter 07. Probability: All Mutations are not Equal (-ly Probable)
• Chapter 08. Bioinformatics Programming: A Primer
• Index