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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 InterProScan5 installation at CSC can be used to search protein signatures from following databases:

  • TIGRFAM (15.0)
  • SFLD (4)
  • SUPERFAMILY (1.75)
  • PANTHER (15.0)
  • Gene3D (4.3.0)
  • Hamap (2020_05)
  • Coils (2.2.1)
  • ProSiteProfiles (2021_01)
  • SMART (7.1)
  • CDD (3.18)
  • PRINTS (42.0)
  • PIRSR (2021_05)
  • ProSitePatterns (2021_01)
  • AntiFam (7.0)
  • Pfam (34.0)
  • MobiDBLite (2.0)
  • PIRSF (3.10)


Free to use and open source under Apache License 2.0.


  • Puhti: 5.55-88.0


In Puhti, first load interproscan module with commands:

module load biokit
module load interproscan

After that you can submit InterProScan jobs using command cluster_interproscan. Cluster_interproscan is a help tool that automatically runs your InterProScan task using the batch job system of Puhti. If your query file contains several sequences the cluster_interproscan tool also automatically splits the InterProScan tasks to several subtasks that are run simultaneously in Puhti.

cluster_interproscan accepts all the normal InterProScan options. To check the available options, give command:

cluster_interproscan -h

Below is two sample InterProScan commands

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

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

  2. Running InterProScan search for protein sequence set against PfamA databases. Results are reported in GFF3 format. GFF3 conversion needs more memory that what is available in the login nodes of Puhti. Because of that you should submit the interporosacn task from an interactive batch job with least 4 GiB of memory reserved.

    sinteractive -m 4000
    cluster_interproscan -i proteins.fasta -o results.gff3 -f GFF3 -appl PfamA

More information

Last update: October 10, 2022