Prime User Manual - ISP

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Chapter 11: Command Syntax
Command Input File
The command input file consists of lines containing keyword-value pairs, one per line. The
keywords are described in Table 11.9.
Table 11.9. Keywords for the ssp input file.
Keyword syntax Description
QUERY_FILE filename Required. Name of the FASTA file containing the query sequence
METHOD program Required. Name of the secondary structure prediction that is to be run.
Allowed values are sspro, psipred, profking, and all. all means
run all available programs. If the input file contains multiple METHOD keywords,
only the last one is used.
OUTPUT_FILE filename Optional. Name of the output file. Default is jobname.out.
Return Value and Errors
ssp returns 0 if successful and a non-zero value in all other cases.
Environment Variables
The environment variables that can be used to control the secondary structure prediction
programs are listed in Table 11.10.
Table 11.10. Environment variables for secondary structure prediction programs.
Environment Variable Description
PSP_SSPRO_DB BLAST database to be searched when assembling the multiple sequence
alignment used in the SSPro prediction
PSP_PSIPRED_DB BLAST database to be searched when assembling the sequence profile
used in the PSIPRED prediction
Examples
The following minimal input file, called sspro.inp, generates an SSPro secondary structure
prediction for the sequence stored in file query.fasta:
QUERY_FILE query.fasta
METHOD sspro
The prediction produced by the back-end is written to the file sspro.out.
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