WU-BLAST was
developed and is maintained entirely by Warren Gish. He was one of
the original authors of BLAST while at the NCBI but is now at
Washington University in St. Louis (where the WU
comes from). Development began in 1994 at Version 1.4, before BLAST
had gapped alignments. Quite a lot has changed since then.
Paradoxically, WU-BLAST is more similar to the original BLAST than
the current NCBI version.
WU-BLAST is
useful because it has more command-line parameters that allow
advanced users to control the program with more precision. It is also
faster. Table 14-1 displays features unique to
WU-BLAST or significantly different from
NCBI-BLAST.
Table 14-1. WU- and NCBI-BLAST feature differences
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Word size
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Any word size for any program mode. Neighborhood words are turned off
for word sizes of 5 or greater, but may be activated by setting an
explicit value for T.
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blastn has a minimum word size of 7.
blastp, blastx,
tblastn, and tblastx have
word sizes of 2 or 3. Neighborhood words are never used for
blastn.
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Nucleotide scoring
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Choice of match/mismatch or scoring matrix.
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Only match/mismatch scoring.
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Nucleotide statistics
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Karlin-Altschul parameters are available for several match/mismatch
values and gap costs.
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Karlin-Altschul parameters are always computed without respect to gap
costs. Reported E-values may greatly overestimate significance.
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altscore
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Allows score modification for any matrix (e.g., to set stop scores
lower).
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Nothing similar.
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H, K, L,
gapH, gapK,
gapL
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Especially useful when using unsupported scoring schemes; allow the
provision of values for Karlin-Altschul parameters.
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Nothing similar. Unsupported scoring schemes are fatal errors.
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Alias databases
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No, but virtual databases offer similar functionality.
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Yes, both alias and virtual databases are supported.
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Gapped alignment
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All programs.
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All programs except tblastx.
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/etc/sysblast
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Allows systems administrators to set system-wide resource
restrictions.
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Nothing similar.
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Database subset selection
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Yes, via dbrecmin and dbrecmax.
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No, but alias databases can be used for static splitting.
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Restricted region of query
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The nwstart and nwlen
parameters restrict seeding but not alignment.
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-L restricts both seeding and alignment.
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links
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Displays the order of alignments in a group.
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Nothing similar.
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topcomboN
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Allows restriction of number alignment groups. Groups are clearly
labeled.
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Nothing similar.
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kap
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Computes significance without sum statistics.
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Nothing similar.
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olf, golf,
olmax, golmax
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Allows setting of overlap rules for HSP consistency.
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Fixed internally.
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notes, warnings,
errors
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Descriptive messages at various levels ofcaution.
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Most error messages are terse and not user friendly.
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Output formats
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Only the standard format.
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Multiple output report formats including HTML, ASN.1, XML, tabular,
and anchored multiple alignments. See Appendix A.
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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 commercial users must pay a fee. Unlike NCBI-BLAST,
the source code isn't freely available. 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.
