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Analyses

This page lists the analyses available in InterProScan 6 and the names accepted by --applications and --skip-applications.

Tip

Analysis names are case-insensitive, and hyphens, underscores, and spaces are ignored. For example, CATH-Gene3D, cathgene3d, and CATH_GENE3D are all valid.

Analysis catalogue

Analysis Description Included by default Requires separate licensed application
AntiFam Identifies sequences likely to be spurious or misannotated Yes No
CATH-Gene3D Identifies structural domains from the CATH classification Yes No
CATH-FunFam Groups protein domains into functional families based on CATH Yes No
CDD Detects conserved domains using position-specific scoring matrices from NCBI Yes No
COILS Predicts coiled-coil regions based on sequence patterns Yes No
DeepTMHMM Predicts transmembrane helices No Yes
HAMAP Identifies high-confidence protein families in microbial and organellar proteomes Yes No
MobiDB-lite Predicts intrinsically disordered regions Yes No
NCBIFAM Matches proteins to curated HMMs from NCBI, including TIGRFAMs Yes No
PANTHER Classifies proteins into families and subfamilies with curated GO terms Yes No
Pfam Detects protein domains and families using HMMs built from multiple sequence alignments Yes No
Phobius Predicts transmembrane topology and signal peptides No Yes
PIRSF Classifies proteins into evolutionary families based on full-length sequence similarity Yes No
PIRSR Identifies conserved residues using manually curated site rules Yes No
PRINTS Detects protein families using groups of conserved motifs Yes No
PROSITE-patterns Identifies protein features based on short sequence motifs Yes No
PROSITE-profiles Detects protein families and domains using position-specific scoring profiles Yes No
SFLD Classifies enzymes by relating sequence features to chemical function Yes No
SMART Identifies signaling and extracellular domains Yes No
SUPERFAMILY Assigns structural domains using HMMs based on the SCOP superfamily classification Yes No
SignalP-Euk Predicts signal peptides in eukaryotic proteins No Yes
SignalP-Prok Predicts signal peptides in prokaryotic proteins No Yes
TMbed Predicts transmembrane helices, transmembrane strands, and signal peptides No No

Default selection behaviour

  • By default, InterProScan runs all analyses except the deep-learning-based analyses (DeepTMHMM, SignalP-Euk, SignalP-Prok, and TMbed).
  • DeepTMHMM, SignalP-Euk, SignalP-Prok, and TMbed are only run when explicitly selected with --applications, or when you use --run-ml.
  • Phobius is not a deep-learning-based analysis, but it still requires separate installation before it becomes available.

Licensed applications

Some InterProScan analyses rely on separately licensed third-party applications.

This affects the external software component, not your ability to run InterProScan itself or to analyse your own sequences with the bundled analyses.

The licensed analyses are:

  • DeepTMHMM
  • Phobius
  • SignalP-Euk
  • SignalP-Prok

See Licensed applications for installation and activation instructions.

Changes from InterProScan 5

InterProScan 6 supports most of the analyses available in InterProScan 5.

The following analyses were available in InterProScan 5 but are not included in InterProScan 6:

Name Reference Description
SignalP 4 Petersen et al., 2011 Prediction of the presence and location of signal peptide cleavage sites
TMHMM Krogh et al., 2001 Prediction of transmembrane helices

InterProScan 6 also adds the following analyses:

Name Reference Description
DeepTMHMM Krogh et al., 2001 Prediction of transmembrane helices
SignalP 6 Teufel et al., 2022 Prediction of signal peptides and their cleavage sites in all domains of life
TMbed Bernhofer & Rost, 2022 Prediction of transmembrane proteins through Language Model embeddings