InterProScan

InterProScan is a tool that compares protein or nucleotide sequence against a set of protein signature databases. The results obtained from different databases are given in uniform format. The InterProScan 5 installation on Roihu can be used to search protein signatures from the following databases:

• AntiFam
• CDD
• FunFam
• Gene3D
• HAMAP
• NCBIfam
• PANTHER
• Pfam
• PIRSF
• PIRSR
• PRINTS
• PROSITE (patterns and profiles)
• SFLD
• SMART
• SUPERFAMILY

The analyses that require a separate license (Phobius, SignalP and TMHMM) are not available. To see the available analyses and their database versions, run interproscan.sh -h.

• InterProScan
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source under Apache License 2.0.

Available

• Roihu-CPU: 5.76-107.0, via the bio-apps module.

Usage

InterProScan is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the InterProScan module:

module load bio-apps/v202603
module load interproscan/5.76-107.0

The InterProScan data is installed in a shared location on Roihu. The module sets the INTERPROSCAN_CONF environment variable to a configuration file that points InterProScan to this data, so you don't need to download or configure anything yourself.

InterProScan is run with the interproscan.sh command. To check the available options, give the command:

interproscan.sh -h

Below are two sample InterProScan commands:

1. Running InterProScan search for a nucleotide sequence set against all InterProScan databases. Results are reported in XML format.

interproscan.sh -i nucleotides.fasta -o results.xml -f XML -t n

1. Running InterProScan search for a protein sequence set against Pfam. Results are reported in GFF3 format.

interproscan.sh -i proteins.fasta -o results.gff3 -f GFF3 -appl Pfam

The interproscan.sh launcher reserves up to 14 GB of memory for Java alone, so don't run InterProScan on the login nodes. Use an interactive session with enough cores to get the memory, for example sinteractive --account <project> --cores 12 --time 04:00:00 (about 22 GB), or a batch job.

Example batch script

#!/bin/bash
#SBATCH --job-name=interproscan
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G

module load bio-apps/v202603
module load interproscan/5.76-107.0

interproscan.sh -i proteins.fasta -o results.tsv -f TSV -cpu $SLURM_CPUS_PER_TASK

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• InterPro home page
• InterProScan documentation

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