BLAST

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Chapter 13: NCBI-BLAST Reference

formatdb -i db -o T -V t

formatdb -i db -o -V

formatdb -idb -ot -VT

formatdb -idb -o -V

The following command, however, is illegal because it tries to set -o to a value of V.

formatdb -idb -oV

blastall Parameters

blastall is controlled by several parameters. Many of the parameters have default set-

tings and don’t need to be explicitly assigned. Consider this simple command:

blastall -p blastp

Behind the scenes, this command is converted to:

blastall -p blastp -d nr -i stdin -e 10 -m 0 -o stdout -F T -G 11 -E 2 -X 15 -v 500

-b 250 -f 11 -g T -a 1 -M BLOSUM62 -W 3 -z 0 -K 0 -Y 0 -T F -U F -y 0.0 -Z 0 -A 40

You can see that many parameters are set without your express knowledge. These

parameters affect the results of your experiment and, as reinforced many times

throughout the book, you should try to understand these parameters and set them to

fit each experiment.

The following reference section explains all the parameters available for blastall and

lists the default values that are used if not explicitly set. The table was compiled

according to the default values for the five basic programs. Although megablast can

be run from within blastall (

-n T), you should use the standalone program. The

parameters for it are presented later in the chapter.

-a [integer]

Default: 1

Programs: All

Sets the number of processors to use on of processors. If you have multiple queries, you

will get better throughput by executing multiple BLAST searches. For insensitive searches

such as default BLASTN, setting

-a to a higher value may not appreciably improve speed if

disk I/O is the bottleneck.

-A [integer]

Default: blastn 0, others 40

Programs: All

Sets the multiple-hit window size. When BLAST is set to two-hit mode, this option requires

two word hits on the same diagonal to be within

[integer] letters of each other in order to

extend from either one. The larger the

[integer], the more sensitive BLAST will be. Setting

[integer] to 0 sets the default behavior of 40, except for blastn, whose default is single

word hit. To specify one-hit behavior, set -

P1.

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blastall Parameters

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-b [integer]

Default: 250

Programs: All

Truncates the report to [integer] number of alignments. There is no warning when you

exceed this limit, so it’s generally a good idea to set

[integer] very high unless you’re inter-

ested only in the top hits.

-B [integer]

Default: Optional

Programs: blastn, tblastn

Sets the number of queries to concatenate in a single search. Concatenating queries acceler-

ates the search because the database is scanned just one time. This is the principle

underlying megablast, but the implementation is different in blastall.

This option is new in Version 2.2.6 and still experimental. The specified

[integer] must be

the number of sequences in the query file. If it’s less, only the first set of

[integer]

sequences is used. Also, the output is very different than you would expect. All the query

names are listed, and then all the one-line summaries are given, followed by the align-

ments, and finally, one footer is produced for the whole report. Given this format, it’s very

difficult to discern which alignments belong to which query. This option should not be

used in its current implementation.

-d [database]

Default: nr

Programs: All

Identifies the database to search. [database] must already be formatted by formatdb.

BLAST looks for

[database] in the following order: the local directory, the BLASTDB envi-

ronment variable (Unix only), and finally, the location specified in the .ncbirc file.

You can merge multiple databases into a single virtual database by putting the individual

databases in quotes. For example, to merge the nt and est databases, use:

-d "nt est". You

can’t mix nucleotide and amino acid databases. The statistics reported are based on the

sizes of the combined databases. Virtual databases may exceed file size limits imposed by

the operating system.

-D [1..23]

Default: 1

Programs: tblastn, tblastx

The genetic code to use for translation of the database nucleotide sequence. See http://

www.ncbi.nlm.nih.gov/htbin-post/Taxonomy for updates.

Options

1 Standard Nuclear Genetic Code

2 Vertebrate Mitochondrial

3 Yeast Mitochondrial

4 Mold, Protozoan, and Coelocoel Mitochondrial