PSIPRED generates secondary structure predictions using up to four feed-forward neural networks and output from PSI-BLAST.

References:

• Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. (1999) 292: 195-202.

• README
• PSIPRED server

• Module Name: PSIPRED (see the modules page for more information)
• Multithreaded
• Environment variables set
  • PSIPRED_HOME
  • PSIPRED_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load PSIPRED
[user@cn3144 ~]$ cp $PSIPRED_EXAMPLES/example.fasta .
[user@cn3144 ~]$ runpsipredplus example.fasta
Running PSI-BLAST with sequence example.fasta ...
Predicting secondary structure...
Pass1 ...
Pass2 ...
Cleaning up ...
Final output files: example.ss2 example.horiz
Finished.
[user@cn3144 ~]$ ls
example.fasta  example.horiz  example.ss  example.ss2

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. PSIPRED.sh). For example:

#!/bin/bash
module load PSIPRED
runpsipredplus my.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] PSIPRED.sh

Create a swarmfile (e.g. PSIPRED.swarm). For example:

runpsipredplus file1.fasta > run1.out
runpsipredplus file2.fasta > run2.out
runpsipredplus file3.fasta > run3.out
runpsipredplus file4.fasta > run4.out

Submit this job using the swarm command.

swarm -f PSIPRED.swarm [-g #] [-t #] --module PSIPRED