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.
70
|
Chapter 4: Sequence Similarity
NCBI-BLAST and WU-BLAST compute combined statistical significance a little dif-
ferently. The previous descriptions apply to NCBI-BLAST only. The two programs
probably have many similarities, but the specific formulations for WU-BLAST are
unpublished.
Probability Versus Expectation
While NCBI-BLAST reports an Expect, WU-BLAST reports both the E-value and a
P-value. An E-value tells you how many alignments with a given score are expected
by chance. A P-value tells you how often you can expect to see such an alignment.
These measures are interchangeable using Equations 4-22 and 4-23.
For values of less than 0.001, the E-value and P-value are essentially identical.
Further Reading
Altschul, S.F. (1991). “Amino acid substitution matrices from an information theo-
retic perspective.” Journal of Molecular Biology, Vol. 219, pp. 555-565.
Altschul, S.F. (1997). “Evaluating the statistical significance of multiple distinct local
alignments.” Theoretical and Computational Methods in Genome Research,S.
Suhai (ed.), pp. 1-14.
Altschul, S.F. (1993). “A protein alignment scoring system sensitive at all evolution-
ary distances.” Journal of Molecular Evolution, Vol. 36, pp. 290-300.
Altschul, S.F., M.S. Boguski, W. Gish, and J.C. Wootton (1994). “Issues in search-
ing ...
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.