InterProScan 6: a modern large-scale protein function annotation pipeline

InterProScan is a widely used software package for large-scale protein function classification and an essential component of UniProt, Ensembl and MGnify Genomes large-scale annotation pipelines. For the past 12 years, InterProScan 5 has provided robust analysis but faced challenges in scalability, installation, data management, and integration with modern workflow systems. We present InterProScan 6, a complete reimplementation as a Nextflow pipeline that enhances scalability, portability, and reproducibility across diverse computational environments, including local, HPC, and cloud platforms. Key improvements include decoupling of application code from signature data, native container support, on-demand data management, integration of modern deep-learning-based predictors, and a redesigned Matches API for retrieving pre-computed annotations in JSON format.

Across nine reference proteomes ranging from bacteria to complex eukaryotes, InterProScan 6 consistently reduced wall-clock runtime relative to InterProScan 5, with speedups of approximately two-fold on large eukaryotic proteomes. When pre-computed annotations were available via the Matches API, runtimes were reduced to minutes. Comparison of annotations generated from all Swiss-Prot sequences shows that InterProScan 6 reproduces InterProScan 5 results with near-identical precision and sensitivity across all InterPro member databases. InterProScan 6 therefore enables more efficient, flexible, and reproducible genome-scale protein function annotation.

InterProScan 6 is distributed under the Apache 2.0 license. Its documentation is hosted on ReadTheDocs (https://interproscan6.readthedocs.io/) and its source code is available on GitHub (https://github.com/ebi-pf-team/interproscan6).