July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Where Did My Oligo Go?
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109
So far in this chapter, we’ve just walked through most basic operations of Karlin-
Altschul statistics to provide you with the knowledge necessary to calculate bit
scores, effective lengths, and Expects. We’ve explained that BLAST uses one statisti-
cal measure to calculate the Expect of an HSP and another to calculate the aggregate
Expect of a group of HSPs. Hopefully, you’ve gained a better understanding of how
all of these operations of fit into the larger picture of Karlin-Altschul statistics.
You have also seen that it’s possible to use Karlin-Altschul statistics to recover statis-
tical measures that are calculated by BLAST internally, but not included in the
report—principally, sum scores and the individual Expect for an HSP for which an
Expect(n) has been reported. Learning to calculate these values is the first step
toward becoming a power user of BLAST statistics. The remaining sections of this
chapter will show you how to use what you’ve learned to deal with critical questions
about BLAST results.
Using Statistics to Understand BLAST Results
Karlin-Altschul statistics is much more than a way to determine the statistical signifi-
cance of a sequence alignment in the context of a database search. It also provides a
framework with which to probe the ...
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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.