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nf-core/proteinfamilies: a scalable pipeline for the generation of protein families
Open accessPublished version of a preprint
Abstract
The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Karatzas, E., Beracochea, M., Baltoumas, F. A., Aplakidou, E., Richardson, L., Fellows Yates, J. A., Lundin, D., community, N.-C., Buluç, A., Kyrpides, N. C., Georgakopoulos-Soares, I., Pavlopoulos, G. A., & Finn, R. D.
- Affiliations
- European Bioinformatics Institute (GB)
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD ,
- Alexander Fleming Biomedical Sciences Research Center (GR)
- University of Crete (GR)
- Max Planck Institute for Evolutionary Anthropology Department of Archaeogenetics, , Deutscher Pl. 6, Leipzig 04103 ,
- Stockholm University (SE)
- Applied Mathematics and Computational Research Division (AMCR), Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, CA 94720 ,
- Lawrence Berkeley National Laboratory (US)
- College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute Division of Pharmacology and Toxicology, , 1400 Barbara Jordan Blvd., Austin, TX 78723 ,
- Mohamed bin Zayed University of Artificial Intelligence (AE)
- Corresponding author
- Finn, Robert D
- ORCID
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2026
- Volume
- 15
- ISSN
- 2047-217X (ISSN-L)
- OpenAlex
- W7125234690
- Cited by
- 0
- References
- 1
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- GigaScience (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- DiVA (Linnaeus University) (submittedVersion, other-oa)
- Funders
- European Union
- Hellenic Foundation for Research and Innovation (DE-AC02-05CH11231)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- protein families, metagenomics, hypothetical protein, protein annotation, multiple sequence alignment, conserved residues, Nextflow pipeline, protein family clustering
- MeSH terms
- Algorithms, Amino Acid Sequence, Proteins, Software, Sequence Alignment, Computational Biology, Databases, Protein, Metagenomics, Molecular Sequence Annotation
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