July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 10: Installation and Command-Line Tutorial
If the data directory can’t be found, blastall reports that it is unable to open the scor-
ing matrix:
Searching[blastall] WARNING: <query> [000.000] Unable to open <matrix>
WU-BLAST
As in the previous section, you’ll run the various components of the WU-BLAST
software in typical sequence analysis settings.
xdformat
Start by formatting the ESTs database with the following command. The -n indi-
cates that this is a nucleotide database. This command creates three files: ESTs.xnd,
ESTs.xns, and ESTs.xnt.
xdformat -n ESTs
xdformat also prints some interesting statistics to stdout. You can always retrieve this
information later with
xdformat -n -r ESTs.
XDFORMAT-WashU 1.0 [02-Apr-2002] [macosx-ppc-ILP32F64 2002-04-02T01:26:43]
Start: 2002-09-29T12:10:05
Input: "ESTs"
XDF Output Database: ESTs
Alphabet: NCBI2na(1)
No. of sequences (letters) written: 2000 (673,456)
Longest sequence written (in database): 933 (933)
Edit Alphabet: WUStLna(1)
Sequences edited for ambiguity codes: 961
No. of edits (total length) written: 1901 (2102)
Index entries written (in database): 2000 (2000)
Total cpu time: 0.12u 0.00s 0.12t Elapsed: 00:00:00
End: 2002-09-29T12:10:05
If you use the free version of WU-BLAST, use pressdb instead of xdformat. The out-
put is
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