ArticleBioinformatics advances2026
InterProScan 6: a modern large-scale protein function annotation pipeline.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
3 citing papers in PubMed.
- Novel Thermophilic Species ofLife (Basel, Switzerland) · 2026Article
- ProteoMapper: Alignment-aware identification and quantitative analysis of contextual motif-domain patterns in protein families.PloS one · 2026Article
- Genomic and structural insights into the high-efficiency poly(3-hydroxybutyrate) biodegradation inFrontiers in microbiology · 2026Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: 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. Results: 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. Availability and implementation: 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).
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.