dbiblast

dbiblast

dbiblast indexes a BLAST database created by the NCBI indexing programs (formatdb, pressdb, or setdb) and builds EMBL CD-ROM format index files.

Here is a sample session with dbiblast, using a BLAST2 protein database:

% dbiblast       NCBI : NCBI with | characters        GCG : GCG format dbname:entryname     SIMPLE : ID and accession         ID : entryname    UNKNOWN : unknown Entry format [unknown]: gcg Database name: swnew Database directory [.]: /nfs/disk42/pmr/emboss/test/blastp2/ database base filename [swnew]: Release number [0.0]: Index date [00/00/00]: 04/02/00          N : nucleic          P : protein          ? : unknown Sequence type [unknown]: p          1 : wublast and setdb/pressdb          2 : formatdb          0 : unknown Blast index version [unknown]: 2

Mandatory qualifiers:

[-dbname] (string)

Database name.

-directory (string)

Database directory.

-filenames (string)

Wildcard database filename.

-release (string)

Release number.

-date (string)

Index date.

-seqtype (menu)

Sequence type.

-blastversion (menu)

BLAST index version.

Advanced qualifiers:

-fields (menu)

Index fields.

-exclude (string)

Wildcard filename(s) to exclude.

-indexdirectory (string)

Index directory.

-sortoptions (string)

Sort options, typically -T . to use current directory for work files, or -k 1,1 to force GNU sort to use the first field.

-maxindex (integer)

Maximum index length.

-[no]systemsort (boolean)

Use system sort utility.

-[no]cleanup (boolean)

Clean up temporary files.

-sourcefile (boolean)

Use FASTA source file.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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