Table of Contents

InterProScan

Description

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
PIRSF
ProDom
SMART
PrositeProfiles
PrositePatterns
HAMAP
PfamA
PRINTS
SuperFamily
Coils
Gene3d

Version

  • InterProScan version 5.36-75.0 is available in Puhti

Usage

In Puhti, first set up the bioinformatics toolkit with command:

module load biokit

The biokit module sets up a set of commonly used bioinformatics tools. Note however that there are also bioinformatics tools in Puhti, that have a separate setup commands.

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
  1. Running InterProScan search for protein sequence set against PfamA databases. Results are reported in GFF3 format.
cluster_interproscan -i proteins.fasta -o results.gff3 -f GFF3 -appl PfamA

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