Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

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.