ABSTRACT

Part I Introduction 2 1. What Is Genome Browser? 2 2. Multiple Genome Browser Sites 2 3. What Can UCSC Genome Browser Do? 5

Part II Step-By-Step Tutorial 19 1. Basic Functionality of Genome Browser and BLAT Use 19 2. Table Browser Use 24 3. Creating and Using Custom Track 26 4. Gene Sorter 32 5. In Silico PCR 32 6. Other Utilities (DNA Duster) 33

Part III Sample Data 34 SECTION 2 SEQUENCE SIMILARITY SEARCHING BY BLAST 35

Part I Introduction 35 1. What Is BLAST? 35 2. What Are the Principles Behind This Software? 36 3. What Can BLAST Do? 39

Part II Step-By-Step Tutorial 45 Part III Sample data 52

Since the launch of the International Human Genome Project and official whole-genome sequencing projects from other species, tremendous amounts of sequence data (>~3.3 million) have become available. In addition, large-scale technologies, such as microarray for gene expression detection and genome-wide association studies, also have speeded up the collection of sequences to the public databases. How to effectively display, align, and analyze genomic sequences to harness genomic power therefore becomes crucial in the postgenomic era. This chapter commences with Genome Browser in Section 1 and then introduces the Basic Local Alignment Search Tools (BLAST) in Section 2. In line with the format and style throughout this book, each section starts with a theoretical introduction in Part I, continues with a step-by-step tutorial in Part II, and ends with the presentation of sample data in Part III.