BLAST

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blastall Parameters

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useful if the settings of -b or -v are low, and the abundant alignments push lower scoring

alignments off the end of the report. If set, a value of 100 is recommended.

-l [file]

Default: Optional

Programs: All

Restricts database search to a list of GIs found in [file]. The database sequences must

have NCBI-compliant identifiers, including GI numbers, and the database must be indexed

(by running formatdb with the

-o option). The [file] must be in the same directory as the

database or in the directory from which blastall is called.

[file] may be in text format with

one GI per line or in binary format (see the

-B parameter for formatdb).

-L [string]

Default: Optional

Programs: All

The location on query sequence. This lets you limit the search to a subsequence of the

query sequence. For example, to search just the letters from 21 to 50, add the following

parameter:

-L "21,50"

The alignments won’t extend outside the specified region. In older versions of BLAST, -L

set the size of the region under control of the -K parameter.

-m [0..11]

Default: 0

Programs: All

Sets the alignment viewing options. Appendix C gives examples of these display options.

Options

0 Pairwise

1 Query-anchored, showing identities, no gaps in query (gaps are shown as a tree-like

thing in subjects), identities ...