Chapter 14. WU-BLAST Reference

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




Word size

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.

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.

Nucleotide scoring

Choice of match/mismatch or scoring matrix.

Only match/mismatch scoring.

Nucleotide statistics

Karlin-Altschul parameters are available for several match/mismatch values and gap costs.

Karlin-Altschul parameters are always computed without respect to gap costs. Reported E-values may greatly overestimate significance.


Allows score modification for any matrix (e.g., to set stop scores lower).

Nothing similar.

H, K, L, gapH, gapK, gapL

Especially useful when using unsupported scoring schemes; allow the provision of values for Karlin-Altschul parameters.

Nothing similar. Unsupported scoring schemes are fatal errors.

Alias databases

No, but virtual databases offer similar functionality.

Yes, both alias and virtual databases are supported.

Gapped alignment

All programs.

All programs except tblastx.


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.


Displays the order of alignments in a group.

Nothing similar.


Allows restriction of number alignment groups. Groups are clearly labeled.

Nothing similar.


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 ofcaution.

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.

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 If you want to try WU-BLAST, an early version is available without license.