BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

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Preface

The second half of the 20th century was witness to incredible advances in molecular

biology and computer technology. Only 50 years after identifying the chemical struc-

ture of DNA (1953), the sequence of the human genome has been determined and

can be downloaded to a computer small enough to fit in your hand. The pace of sci-

ence can be truly dizzying. So what do you do when you literally have the book of

life in the palm of your hand? Well, you read it of course. Unfortunately, it’s much

easier to read the book of life than to understand it, and one of the great quests of

the 21st century will be unraveling its mysteries. One particularly fruitful approach

to deciphering the book of life has been through comparative studies, such as those

between mouse and human.

Comparisons between the human and mouse genomes show how little has changed

since humans and mice last shared a common ancestor around 75 million years ago.

Very few genes are unique to humans or mice, and in general the genes are more

than 80% identical at the sequence level. However, genes account for a small frac-

tion of these genomes and the majority of sequence is not recognizably similar. This

is where BLAST, the Basic Local Alignment Search Tool, comes in. BLAST is useful

for finding similarities between biological sequences, be they DNA, RNA, or pro-

tein. Sequence similarity is often an indication of conserved function, and you can

use comparative sequence analysis to understand biological sequences in much the

same way that ancient Greeks used comparative anatomy to understand the human

body or that linguists used the Rosetta Stone to understand Egyptian hieroglyphs.

Audience for This Book

People interested in BLAST come from many disciplines including biology, chemis-

try, computer science, law, mathematics, medicine, physics, etc. One reason for this

is that knowledge of genes and genomes is becoming increasingly useful in a variety

of settings. Another reason is that bioinformatics is this century’s rocket science.

Researchers from many disciplines are being drawn into its fascinating and rapidly