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BLAST by Joseph Bedell, Mark Yandell, Ian Korf

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This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
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Chapter 14: WU-BLAST Reference
To use the most recent version of WU-BLAST, you must have a site license from
Washington University in St. Louis. The product is free for academic use, but com-
mercial users must pay a fee. Unlike NCBI-BLAST, the source code isn’t freely avail-
able. For the latest information on WU-BLAST, visit the official site at http://blast.
wustl.edu. If you want to try WU-BLAST, an early version is available without
license.
Usage Statements
All WU-BLAST programs provide usage statements if they are executed without any
arguments. They are sometimes lengthy, so it’s best to pipe them through a pager
such as less or more.
blastn | more
xdformat | less
xdget | less
Command-Line Syntax
WU-BLAST command-line syntax isn’t uniform between all programs. The BLAST
programs blastn, blastp, blastx, tblastn, and tblastx use a slightly different syntax than
do xdformat, and xdget.
/etc/sysblast Allows systems administrators to set system-
wide resource restrictions.
Nothing similar.
Database subset selection Yes, via
dbrecmin and dbrecmax. No, but alias databases can be used for static
splitting.
Restricted region of query The
nwstart and nwlen parameters
restrict seeding but not alignment.
-L restricts both seeding and alignment.
links
Displays the order of alignments in a group. Nothing similar.
topcomboN
Allows restriction of number alignment
groups. Groups are clearly labeled.
Nothing similar.
kap
Computes significance without sum statistics. Nothing similar.
olf, golf, olmax,
golmax
Allows setting of overlap rules for HSP
consistency.
Fixed internally.
notes, warnings,
errors
Descriptive messages at various levels of
caution.
Most error messages are terse and not user
friendly.
Output formats Only the standard format. Multiple output report formats including
HTML, ASN.1, XML, tabular, and anchored
multiple alignments. See Appendix A.
Table 14-1. WU- and NCBI-BLAST feature differences (continued)
Feature WU-BLAST NCBI-BLAST

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