InterProScan documentation

Contents:

• Introduction
  • What is InterProScan?
  • Supported platforms
  • To install and run InterProScan
    • LSF cluster users
• Release notes: InterProScan 5.70-102.0
  • What’s new
    • Data update
    • Software updates
    • Known issues
    • Reporting issues
• Installation requirements
  • How to check these on a system?
    • Which version of Linux am I running?
    • Testing your Perl installation
    • Testing your Python installation
    • Testing the Java environment
• Obtaining a copy of InterProScan
  • Obtaining the core InterProScan software
  • Index hmm models
  • Panther models
  • Using the Local Pre-calculated Match Lookup Service (optional)
• Running InterProScan
  • InterProScan test run
  • Command-line options
    • -dp / –disable-precalc (optional)
    • -appl / –applications application_name (optional)
    • -i / –fasta sequence_file
    • -iprlookup,–iprlookup
    • -goterms,–goterms (optional)
    • -b / –output-file-base file_name (optional)
    • -o / –outfile (optional)
    • -pa / –pathways (optional)
    • -t / –seqtype (optional)
    • -T / –tempdir (optional)
    • -dra / –disable-residue-annot (optional)
    • -version / –version (optional)
  • Included analyses
  • Output format
  • Optional configuration
    • Working directory for temporary files
    • Configuring the Pre-calculated Match Lookup Service
  • Running InterProScan on an LSF/SGE Cluster
• How to Use InterProScan via Container
  • Get InterProScan data
  • Using Docker
    • Example:
  • Using Singularity
    • Example:
• Input formats
  • Supported input file format
  • Supported sequence format
• Output formats
  • Tab-separated values format (TSV)
    • Example output
  • Extensible Markup Language (XML)
    • Example output
  • The XML Schema Definition
  • JavaScript Object Notation (JSON)
    • Example output
  • Generic Feature Format Version 3 (GFF3)
    • Example output
• Nucleic acid sequences scan
  • The Open Reading Frame prediction tool
  • How can I scan nucleic acid sequences in InterProScan 5?
  • Which output formats are supported?
  • Redundant sequences and identifiers in your FASTA file
  • Improving performance
    • Selecting the ORFs to analyse
• The InterProScan Lookup Match Service
  • Installing the lookup service locally
  • System requirements
  • Obtaining the lookup service
    • Run with graphical user interface (to set port number)
    • Run “Headless” (no graphical user interface)
  • Waiting for the lookup service to start
  • Testing the service
  • Configure InterProScan 5 to use your local lookup service
• Running InterProScan 5 in Cluster Mode
  • Initial Setup
    • Cluster submission commands
    • Master configuration options
  • Example usage on an LSF, SGE and other clusters
  • clusterrunid
  • In house tested cluster versions
  • Related issues
• Running InterProScan 5 in CONVERT mode
  • Usage instructions
  • Example Usage
• Improving performance
  • Review your CPU (and memory) command options
  • Consider chunking large input files
  • Review your command line input options
    • Running InterProScan in CLUSTER mode
  • Configure to analyse fewer ORFs (applies to nucleic acid sequences only)
• Activating Phobius/SignalP/TMHMM analyses
  • Phobius
  • SignalP
  • TMHMM
• Providing your feedback
  • Support requests
  • General discussion and suggestions
• Known issues
  • Open issues in InterProScan
    • 1. CDD/RPSBlast errors
    • 2. Coils errors
    • 3. Prosite/pfsearchV3 errors
    • 4. HMMER errors
    • Contacting us
• FAQ
  • What should I do if one of the binaries included with InterProScan doesn’t work on my system?
  • Where can I find the XSD of the XML output?
  • Can I use different binary versions than listed?
  • Which cluster does InterProScan support?
  • Is there Galaxy has a wrapper for InterProScan?
    • Documentation and contact details
    • Publication
  • 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”?
  • How is InterProScan 5 different from InterProScan 4? How do I migrate?
• Installing and compiling binaries used in Interproscan
  • cath-resolve-hits (used by CATH-Gene3D)
  • PfscanV3/PfsearchV3 (used by ProSite Profiles, ProSite Patterns and HAMAP)
  • Hmmer 2 (used by SMART)
  • Hmmer 3 (used by CATH-Gene3D, HAMAP, PANTHER, Pfam, PIRSF, SFLD, SUPERFAMILY and NCBIFAM)
  • ncoils (used by Coils)
  • fingerPRINTScan (used by PRINTS)
  • rpsblast/rpsbproc (used by CDD)
  • sfld_preprocess/sfld_postprocess (used by SFLD)
  • Phobius, TMHMM or SignalP
• Configuration Options
• Cluster mode benchmark run
  • Benchmark run setup
    • Which version of InterProScan 5 (I5) was used for this run?
    • How was the set of input sequences assembled for this run?
    • Which I5 command was used for this run?
    • How does the interproscan.properties file look like?
    • On which cluster/farm did we run I5?
  • Benchmark run outcome
• Change log for InterProScan JSON output format
  • InterProScan 5.31-70.0
• Citing InterProScan
  • Latest publications
    • InterPro
    • InterProScan
  • All previous publications
• Contact us

Indices and tables

• Index

• Module Index

• Search Page