InterProScan 6

InterPro is a database that brings together predictive information on protein function from multiple partner resources. It provides an integrated view of the families, domains and functional sites to which a given protein belongs.

InterProScan is the command‑line tool that allows you to scan protein or nucleotide sequences against the InterPro member‑database signatures in a single workflow. Researchers with novel sequences can use InterProScan to annotate their data with family classifications, domain architectures and site predictions.

Installation

Before you begin, install:

• Nextflow 25.10 or later
• A container runtime. The currently supported are:
  • Docker
  • SingularityCE
  • Apptainer

You don't need anything else, Nextflow will download the workflow from GitHub, and required data are automatically downloaded when running InterProScan.

Important

Some InterProScan analyses rely on third-party applications that require separate licenses and downloads. This does not mean you need a license to run InterProScan itself or to analyse your own sequences with the bundled analyses.

Usage

Quickstart

If you have Docker and Nextflow installed, you can quickly test InterProScan and download the required data by running:

nextflow run ebi-pf-team/interproscan6 \
  -r 6.0.1 \
  -profile docker,test \
  --datadir data \
  --interpro latest

Explanation of parameters:

• -r 6.0.1: Specifies the version of InterProScan to run. We strongly recommend always specifying a version to ensure consistent and reproducible results.
• -profile docker,test:
  • docker: Executes tasks in Docker containers.
  • test: Uses a small test FASTA file included in the workflow.
• --datadir data: Sets the data directory as the location to store InterPro and member database files. The directory will be created automatically if it doesn't exist, and required files will be downloaded into it.
• --interpro latest: Uses the latest available InterPro data release.

Note

While --interpro latest is the default, we strongly recommend pinning a specific version (e.g. --interpro 107.0) to ensure reproducibility.

After the run completes, the following files will be created in your working directory:

• test.faa.gff3: Annotations in GFF3 format
• test.faa.json: Full annotations in JSON format
• test.faa.jsonl: Full annotations in JSON Lines format (one line for each input sequence)
• test.faa.tsv: Tabular summary of matches (TSV format)
• test.faa.xml: Full annotations in XML format

The JSON, JSON Lines, and XML outputs are more comprehensive, the TSV is a concise summary, and the GFF3 is a standard format suitable for genome browsers and annotation pipelines.

Scanning your own sequences

To annotate your own sequences FASTA file, omit the test profile and specify --input:

nextflow run ebi-pf-team/interproscan6 \
  -r 6.0.1 \
  -profile docker \
  --datadir data \
  --input /path/to/sequences.faa

For nucleotide sequences, add --nucleic:

nextflow run ebi-pf-team/interproscan6 \
  -r 6.0.1 \
  -profile docker \
  --datadir data \
  --input /path/to/sequences.fna \
  --nucleic

Documentation

Our full documentation is available on ReadTheDocs.

Support

For further assistance, please create an issue or contact us.

Citation

If you use InterProScan in your work, please cite the following publications:

Blum M, Hobbs E, Florentino L, Bateman A. InterProScan 6: a modern large-scale protein function annotation pipeline. Bioinform Adv. 2026 May 21;6(1):vbag141. doi: 10.1093/bioadv/vbag141.

Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, Marchler-Bauer A, Meng-Papaxanthos L, Mi H, Natale DA, Orengo CA, Pandurangan AP, Piovesan D, Rivoire C, Sigrist CJA, Thanki N, Thibaud-Nissen F, Thomas PD, Tosatto SCE, Wu CH, Bateman A. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 2025 Jan;53(D1):D444-D456. doi: 10.1093/nar/gkae1082.