BLAST

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xdget Parameters

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Index all identifiers.

0 Don’t index.

1 Index only field 1.

2 Index only field 2.

Here are some examples:

-T emb0 doesn’t index EMBL records.

-T gb1 indexes GenBank accession but not locus.

-T gb2 indexes GenBank locus but not accession.

-T gb index both accession and locus of GenBank records.

-v

Default: Off

Sets a user-defined version string for the database (a maximum of 63 characters).

See also

-d

-X

Default: Off

Databases that are formatted but not indexed may be indexed or re-indexed (e.g., with a

different indexing scheme) with

-X. In the following examples, the two commands on Line

1 are equivalent to the one on Line 2.

xdformat -n nt_db ; xdformat -n -X nt_db

xdformat -n -I nt_db

xdget Parameters

xdget retrieves files in FASTA format from databases formatted with xdformat (not

formatdb, pressdb,orsetdb). The database must have been indexed prior to using

xdget (see

-I and -X in the previous section “xdformat Parameters”).

Here are a few example command lines. If identifiers contain vertical bars, as in the

second example, you have to enclose the string in quotes to prevent the shell form

interpreting them as pipes. This isn’t required for identifier files.

xdget -n db 12345

xdget -p nr 'gi|11611819|gb|AAG39070.1|'

xdget -n -f db files_of_ids

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