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.
128
|
Chapter 8: 20 Tips to Improve Your BLAST Searches
8.17 Perform Pilot Experiments
Before embarking on a large BLAST experiment, first try some pilot experiments. For
example, if you want to compare all human proteins to all nonhuman proteins, try
100 proteins first. Or, if you want to annotate a 5 mb chromosomal region with
BLASTX similarities, search 100 Kb first. If you’re unsure of which parameters to
use, try several and see which ones give you the kinds of results you’re looking for. It
may seem like a waste of time, but performing pilot experiments will actually save
you time in the end.
8.18 Examine Statistical Outliers
In a high-throughput setting, BLAST reports may be huge and number in the thou-
sands. There’s no way you can look at all of them, but for quality control, you
should examine some of them. Keep global statistics on BLAST reports, such as
number of hits per Kb. Statistical outliers may point to general problems that
become more apparent in certain sequences.
8.19 Use links and topcomboN to Make Sense of
Alignment Groups
WU-BLAST has two very useful parameters for displaying alignment groupings.
topcomboN sorts alignments into groups and labels them. The links parameter shows
the order of alignments in a group, which is much like the order of a gene’s exons.
Figure ...
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.