July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
274
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Chapter 14: WU-BLAST Reference
H=[number]
Default: Variable; depends on scoring parameters
Sets the value of the Karlin-Altschul parameter H.
See also
gapH, K, gapK, L, gapL
hspmax=[integer]
Default: 1000
Sets the maximum number of ungapped alignments per subject sequence. A warning is
issued if this limit is exceeded. A value of 0 implies no limit.
See also
gspmax
hitdist=[integer]
Default: 0, off
Maximum distance between word hits for the two-hit seeding algorithm. WU-BLAST uses
one-hit seeding by default.
hspsepqmax=[int]
Default: Unlimited
Maximum separation allowed between alignments along the query.
hspsepsmax=[int]
Default: Unlimited
Maximum separation allowed between alignments along the subject.
K=[number]
Default: Variable; depends on scoring parameters
Sets the value for K from the Karlin-Altschul equation.
See also
gapK, H, gapH, L, gapL
kap
Default: Off
Assesses individual alignment scores with Karlin-Altschul statistics rather than using sum
statistics on groups of alignments.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
WU-BLAST Parameters
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275
L=[number]
Default: Variable; depends on scoring parameters
Sets lambda (nats ...
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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.