July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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xdformat Parameters
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281
wordmask=[method]
Default: Off
Filters the query sequence for seeding only. Low-complexity region in the query sequence
isn’t used in the initial word search but is available for alignment during the extension
stage; called soft masking.
See also
filter, lcfilter, lcmask, echofilter, maskextra
W=[integer]
Default: 11 blastn, 3 others
Sets the word size for seeding alignments.
See also
T, hitdist, wink
X=[integer]
Default: Variable; depends on scoring parameters
Controls the alignment extension cutoff for ungapped alignments.
See also
gapX
Y=[number]
Default: Variable; depends on scoring parameters
Sets the size of the query sequence.
See also
Z
Z=[number]
Default: Variable; depends on scoring parameters
Sets the size of the database in letters (restest is assumed), but Z may also be used to mean
the number of sequences if
seqtest is set.
See also
Y, seqtest, restest
xdformat Parameters
xdformat formats BLAST databases from FASTA files. It also reports descriptive
information about the database and dumps the entire content to FASTA format.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
282
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Chapter 14: WU-BLAST Reference ...
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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.