Prime User Manual - ISP

Table 11.2. Keywords for the blast script (Continued)
Keyword Description
Return Value and Errors
blast returns 0 if successful and a non-zero value in all other cases.
Examples
Chapter 11: Command Syntax
MATRIX type Sequence similarity matrix to use for the alignments. Allowed values
of type are BLOSUM45, BLOSUM62, BLOSUM80, PAM30, PAM70
MAX_ROUNDS n Maximum number of passes to use in multipass version (PSI-Blast
–j option); only applies to runs using PROGRAM blastpgp
E_VALUE_THRESHOLD value e-value threshold for inclusion in multipass model (PSIBlast -h
option).
OUTPUT_FILE filename Name of the output file. Default: jobname.out.
PROGNAME name Type of blast search to run. The allowed values are blastp,
blastpgp, and bl2seq (for pairwise alignments). Default: blastp.
TEMPLATE_FILE filename Name of the FASTA file that contains the template sequence
(bl2seq –j option). Only applies to pairwise alignments using
bl2seq
PSSM_ASCII_OUTFILE
filename
EXPAND_HITS {true |
false}
The following is an example input file; query.aa is the query sequence in FASTA format.
QUERY_FILE query.aa
PROGNAME blastp
DATABASE pdb
Environment Variables
ASCII output file for PSI-BLAST matrix (PSIBlast -Q option).
Expand redundant hits, based on information in the NCBI define for a
particular hit. Only available when using Maestro format.
SHOW {all | pdb} Allows the user to restrict the types of hits that are included in the
output. all includes all hits; pdb only includes hits from the PDB.
Only available when using Maestro format.
The following environment variables are supported by the blast script:
PSP_BLASTDB directory containing the customized Blast databases
PSP_BLAST_DIR directory containing a custom Blast installation
Prime 2.1 User Manual 87