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InterProScan

InterProScan

Description

InterProScan is a tool that compairs 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


Available

Version on CSC's Servers


Taito: interproscan5 (5.26-65.0)
FGI grid: interproscan5


Usage

Running InterProScan in Taito

In Taito, 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 Taito, 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 Taito. 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 the Taito cluster. 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.
cluster_interproscan -i proteins.fasta -o results.gff3 -f GFF3 -appl PfamA

Running InterProScan in FGI grid environment.

In Taito, you can send InterProScan jobs to FGI grid environment with command

grid_interproscan

This command works much like the cluster_interproscan command described above. Grid approach is recommended for very large interproscan runs.


Discipline

Biosciences

References


Support

servicedesk@csc.fi


Manual