BLAST

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WU-BLAST Parameters

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The BLAST program options come after the mandatory arguments of database and

query sequence. The command-line structure is as follows:

[program name] [blast database] [query sequence] [parameters]

The parameter names in the BLAST programs and their arguments have some flexi-

bility. The following command lines are all identical:

blastn db query E=10

blastn db query -E 10

blastn db query E 10

blastn db query -E=10

This book uses the first form to avoid confusion with NCBI-BLAST.

xdformat and xdget use the traditional Unix syntax where the parameters precede the

mandatory arguments:

[program name] [parameters] [mandatory arguments]

The xdformat and xdget options are all single letters preceded by a single dash. For

parameters that require a value, a space between the parameter and its value is

optional. As is typical for Unix programs, a double dash indicates the end of com-

mand-line options and a single dash signifies stdin.

xdformat -p protein_db

xdformat -n -I nucleotide_db

zcat fasta.*.gz | xdformat -n -o my_db -- -

WU-BLAST Parameters

WU-BLAST has many control parameters, some of which are esoteric and rarely use-

ful. The most important parameters are listed here.

altscore=[string]

Default: Off

Defines an alternate scoring system for any pair of letters. For example, ...