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.
291
Appendix A
APPENDIX A
NCBI Display Formats
NCBI-BLAST has several options for displaying sequence alignments. These options
are available for the five basic BLAST programs (BLASTN, BLASTP, BLASTX,
TBLASTN, TBLASTX), PSI-BLAST, PHI-BLAST, and MegaBLAST. For all pro-
grams, these formats are selected by using the –
m option; however, in MegaBLAST,
the formats must first be set with the –
D2option to use classic BLAST formatting.
The next section gives a brief description of each option, followed by a detailed
explanation and an example.
Brief Descriptions
The alignment display format is set with the –m option followed by a number from 0
to 11 as you can see in the following table.
Detailed Descriptions and Examples
This section includes detailed descriptions of each format, followed by an example.
To create the examples, the authors performed a BLASTP search of the coelacanth
HoxA11 protein sequence (AAG39070) versus the HoxDB.pep database, which is
included in the online supplement.
Option number Brief description
0 The default pairwise display. Classic BLAST format.
1-6 Various types of query-anchored multiple sequence alignments. The query is anchored and the aligned
regions of the subjects are displayed underneath.
7 eXtensible Markup Language (XML) output.
8 Tabular output, without header ...
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.