BLAST

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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