ArticleBioinformatics (Oxford, England)2018
HFSP: high speed homology-driven function annotation of proteins.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- WASP: a pipeline for functional annotation prediction based on AlphaFold structural models.Nature communications · 2026Article
- On the state of protein function prediction: a report on the fourth CAFA challenge.bioRxiv : the preprint server for biology · 2026Article
- Single-cell transcriptomics reveals lateral transfers of multiple functional genes from prokaryotes to free-living ciliated protists in detrital food webs.Marine life science & technology · 2026Article
- Overcoming extrapolation challenges of deep learning by incorporating physics in protein sequence-function modeling.PLoS computational biology · 2026Article
- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.Biochemistry · 2025Review
- Overcoming Extrapolation Challenges of Deep Learning by Incorporating Physics in Protein Sequence-Function Modeling.bioRxiv : the preprint server for biology · 2025Article
- De novo discovery of conserved gene clusters in microbial genomes with Spacedust.Nature methods · 2025Article
- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.ArXiv · 2025Article
- Cutting-edge deep-learning based tools for metagenomic research.National science review · 2025Review
- Activity-based protein profiling reveals both canonical and novel ubiquitin pathway enzymes in Plasmodium.PLoS pathogens · 2025Article
- Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools.Bioinformatics (Oxford, England) · 2025Article
- Engineering a bacterial toxin deaminase from the DYW-family into a novel cytosine base editor for plants and mammalian cells.Genome biology · 2025Article
- Biological databases in the age of generative artificial intelligence.Bioinformatics advances · 2025Article
- PLMSearch and PLMAlign: Protein Language Model (PLM)-Based Homologous Protein Sequence Search and Alignment.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evaluation of Three Mutations in Codon 385 of Glucose-6-Phosphate Dehydrogenase via Biochemical and In Silico Analysis.International journal of molecular sciences · 2024Article
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings.Bioinformatics (Oxford, England) · 2024Article
- A large-scale assessment of sequence database search tools for homology-based protein function prediction.Briefings in bioinformatics · 2024Article
- PLMSearch: Protein language model powers accurate and fast sequence search for remote homology.Nature communications · 2024Article
- Fast and accurate protein structure search with Foldseek.Nature biotechnology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Motivation: The rapid drop in sequencing costs has produced many more (predicted) protein sequences than can feasibly be functionally annotated with wet-lab experiments. Thus, many computational methods have been developed for this purpose. Most of these methods employ homology-based inference, approximated via sequence alignments, to transfer functional annotations between proteins. The increase in the number of available sequences, however, has drastically increased the search space, thus significantly slowing down alignment methods. Results: Here we describe homology-derived functional similarity of proteins (HFSP), a novel computational method that uses results of a high-speed alignment algorithm, MMseqs2, to infer functional similarity of proteins on the basis of their alignment length and sequence identity. We show that our method is accurate (85% precision) and fast (more than 40-fold speed increase over state-of-the-art). HFSP can help correct at least a 16% error in legacy curations, even for a resource of as high quality as Swiss-Prot. These findings suggest HFSP as an ideal resource for large-scale functional annotation efforts. Supplementary information: Supplementary data are available at Bioinformatics online.
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