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] ...