BLAST

The fact that the human genome is often referred to as the Book of Life is an apt
description because nucleic acids and proteins are often represented (and manipulated)
as text files. Chapter 3 described common algorithms for aligning sequences of
letters, and score is the metric used to determine the best alignment. This chapter
shows what scores really are. Some of the introduced terms come from information
theory, so the chapter begins with a brief introduction to this branch of mathematics.
It then explores the typical ways to measure sequence similarity. You’ll see that
this approach fits well with the sequence-alignment algorithms described in
Chapter 3. The last part of the chapter focuses on the statistical significance of
sequence similarity in a database search. The theories discussed in this chapter apply
only to local alignment. There is currently no theory for global alignment