July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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40
Chapter 3
CHAPTER 3
Sequence Alignment
BLAST finds statistically significant similarities between sequences by evaluating
alignments, but how are sequences aligned? In principle, there are many ways to align
two sequences, but in practice, one method is used more often than any other. This
chapter explains this technique with the biologist in mind, without using the mathe-
matical notation and jargon that is usually employed to describe such algorithm.
Divested of unfamiliar language and notation, these algorithms are quite simple.
Finding the optimal alignment between two sequences can be a computationally
complex task. Fortunately, a technique called dynamic programming (DP) makes
sequence alignment tractable as long as you follow a few rules. Rather than have you
struggle with a confusing definition of DP, this chapter demonstrates how the tech-
nique works for sequence alignment and then gets back to the generalities. There are
fundamentally two kinds of alignment: global and local. In global alignment, both
sequences are aligned along their entire lengths and the best alignment is found. In
local alignment, the best subsequence alignment is found. For example, if you want
to find the two most similar sentences between two books, you use local alignment.
If you want to compare
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.