July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 11: BLAST Databases
Sequence Database Management Strategies
There are many useful public sequence databases, and you may have access to some
private ones as well. Because this is a book about BLAST, we assume you want to use
these collections of sequences in BLAST searches. Some sequences may be used as
queries, and others in databases. How are you going to manage them all in a rational
way? Several possible strategies exist, and the correct one for you depends on your
needs and resources. To demonstrate some of the issues, let’s review a typical
sequence analysis scenario.
Suppose a colleague of yours has just found the gene that makes cats go crazy for cat-
nip. She wants to learn more about this gene and comes to you for help because you
are a BLAST expert. The first thing she wants to do is a BLAST search to find out
what vertebrate proteins are similar to this one. Where are you going to get such a
database of proteins? Once you perform the BLAST search, you find several interest-
ing similarities. Your colleague tells you that these are probably all part of a family of
proteins, and she would like to build a phylogenetic tree to determine their relation-
ships to one another. How are you going to get the individual sequences? Finally, she
decides she wants more information ...
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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.