InterProScan documentation

InterProScan is a software tool for analysing protein and nucleotide sequences against the InterPro database, which integrates functional information from multiple member databases to identify protein families, domains, and sites. With InterProScan users can submit sequences in FASTA format and receive results in multiple formats, providing comprehensive insights into their sequences’ functional characteristics.

InterProScan version 6 uses the Nextflow workflow system for deployment. This means InterProScan can be deployed on a system running 64-bit Linux, Windows or MacOS. Additionally, Nextflow enables the integration of InterProScan into HPC schedulers and cloud providers.

Contents:

• Introduction
  • What is InterProScan?
  • Supported platforms
  • To install and run InterProScan
  • Included analyses
• Release notes: InterProScan 6.0.0
  • What’s new
• Installation requirements
  • OS System:
  • System requirements:
  • Software requirements:
• Installing InterProScan
  • [1] Set up InterProScan
  • [2] (Optional) Install licensed software
  • [3] (Optional) Setup a local InterPro Match Lookup Service (MLS)
• Installing Licensed Applications
  • SignalP Prokayte versus Eukaryote
  • SignalP - Changing mode
  • Run SignalP and DeepTMHMM with GPU acceleration
• Running InterProScan
  • The Help Message
  • Default Operation
  • Command-line arguments
  • Moving the work (temporary) directory
  • Understanding the terminal output
• Migrating from InterProScan Version 5 to Version 6
  • New system requirements
  • Downloading and using the databases
  • Running InterProScan: Flag changes
  • Output files
  • Further help
• Runtime profiles
• Input formats
  • Illegal characters
• Output formats
  • General notes
  • TSV: Tab-separated values format
  • JSON: JavaScript Object Notation
  • JSON Line
  • Extensible Markup Language (XML)
• How to Analyse Nucleic Sequences
  • How to scan nucleic acid sequences
  • Improving performance when analysing nucleic acid sequences
• Integrating InterProScan into a Nextflow pipeline
  • Running specific subworkflows
• Precalculated Match Lookup Service
  • Disabling using the Match Lookup Service
  • Using a local precalculated match lookup service
• Improving performance
  • The bulk profile for large data sets
  • Review your CPU and memory command options
  • Consider chunking large input files
  • Increase the queue size
  • Review your command line input options
  • Configure to analyse fewer ORFs (applies to nucleic acid sequences only)
  • Update to Java 19 or 21
• How InterProScan operates under the hood
  • Third party tools
  • Member databases that use HMMER
  • Member databases with specific tools
• Trouble shooting and FAQs
  • How is InterProScan 6 different from InterProScan versions 4 and 5? How do I migrate?
  • I keep running out of memory
  • I get a “permission denied” error
  • InterProScan cannot access or fails to open files for writing
  • Segmentation Fault
  • Where can I find the XSD of the XML output?
  • Can I use different binary versions than listed?
  • Which cluster does InterProScan support?
  • Do I need to run InterProScan in cluster mode?
  • Is there a Galaxy wrapper for InterProScan?
  • I get Java errors on running InterProScan
  • How to analyse a huge amount of protein sequences (>30000)?
  • Should I filter by e-value?
  • Why do I see “Pre-calculated match lookup service failed - analysis proceeding to run locally”?
  • What is the InterPro Match Lookup Service (MLS)
  • Why does InterProScan use hmmsearch not hmmscan?
• Citing InterProScan
  • Latest InterPro and InterProScan publications
  • Member database and third party tool publications
  • Previous InterPro and InterProScan publications
• Contact us: Support requests and providing feedback
  • Support requests
  • General discussion and suggestions