July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.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.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.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.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
75
Chapter 5
CHAPTER 5
BLAST
Previous chapters explored what biological sequences are, how they are aligned, and
how similarity is measured. This chapter discusses BLAST itself. What is BLAST?
The simple answer is that it is a set of programs that search sequence databases for
statistically significant similarities. The details of how BLAST searches for similari-
ties aren’t so easily answered. Searching requires multiple steps and many control-
ling parameters. Understanding the theoretical framework will help you design and
interpret BLAST experiments, and give you a foundation for troubleshooting when
your search produces unexpected results.
The Five BLAST Programs
The five traditional BLAST programs are: BLASTN, BLASTP, BLASTX, TBLASTN,
and TBLASTX. BLASTN compares nucleotide sequences to one another (hence the
N). All other programs compare protein sequences (see Table 5-1).
Table 5-1. Traditional BLAST programs
Program Database Query Typical uses
BLASTN Nucleotide Nucleotide Mapping oligonucleotides, cDNAs, and PCR products to a
genome; screening repetitive elements; cross-species
sequence exploration; annotating genomic DNA; clustering
sequencing reads; vector clipping
BLASTP Protein Protein Identifying common regions between proteins; collecting
related proteins for phylogenetic analyses ...
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.
Read now
Unlock full access
More than 5,000 organizations count on O’Reilly
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
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.