Prime User Manual - ISP

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Chapter 11: Command Syntax
Syntax
$SCHRODINGER/blast jobname [options]
Input is read from the file jobname.inp. Output is written by default to jobname.out.
Options
The blast script accepts the options listed in Table 11.1.
Input File
Keywords control the operation of the blast script, and are listed in Table 11.2. Most
keywords are simply a translation of options available from the blastall or blastpgp
executables distributed by NCBI. For optional keywords, the Blast default values are used.
Since these defaults can differ between different version of Blast they are not listed here.
Table 11.2. Keywords for the blast script
Keyword Description
QUERY_FILE filename Required. Name of the FASTA file containing the input/query
sequence
DATABASE {nr | pdb} Database to be used in the search. In a default installation the two
allowed values are nr and pdb.
ALIGNMENT_FORMAT value Alignment view options (Blast -m option). Allowed values are:
0 pairwise
1 query-anchored showing identities
2 query-anchored no identities
3 flat query-anchored, show identities
4 flat query-anchored, no identities
5 query-anchored no identities and blunt ends
6 flat query-anchored, no identities and blunt ends
7 XML Blast output
8 tabular
9 tabular with comment lines
m2io Maestro format (default)
EXPECT value Expectation value (E) (Blast -e option).
FILTER {true | false} Filter query sequence: DUST with blastn, SEG with others. (Blast
–F option).
GAP_OPEN_COST value Cost to open a gap (Blast -G option)
GAP_EXTEND_COST value Cost to extend a gap (Blast -E option)
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