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UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

https://doi.org/10.1093/bioinformatics/btu739
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Identification and distribution of protein families in 120 completed genomes using Gene3D
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A new disease-specific machine learning approach for the prediction of cancer-causing missense variants
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0097-8485(96)80004-0openalex-snapshot
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1089/cmb.2007.r005openalex-snapshot
Clustered Sequence Representation for Fast Homology Search
inferredcites →https://doi.org/10.1093/bioinformatics/16.5.458openalex-snapshot
RSDB: representative protein sequence databases have high information content
inferredcites →https://doi.org/10.1093/bioinformatics/17.3.282openalex-snapshot
Clustering of highly homologous sequences to reduce the size of large protein databases
inferredcites →https://doi.org/10.1093/bioinformatics/bti386openalex-snapshot
The properties of protein family space depend on experimental design
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btm098openalex-snapshot
UniRef: comprehensive and non-redundant UniProt reference clusters
inferredcites →https://doi.org/10.1093/bioinformatics/btn174openalex-snapshot
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
inferredcites →https://doi.org/10.1093/nar/30.1.276openalex-snapshot
The Pfam Protein Families Database
inferredcites →https://doi.org/10.1093/nar/gkh097openalex-snapshot
PIRSF: family classification system at the Protein Information Resource
inferredcites →https://doi.org/10.1093/nar/gkr1065openalex-snapshot
The Pfam protein families database
inferredcites →https://doi.org/10.1093/nar/gkr948openalex-snapshot
InterPro in 2011: new developments in the family and domain prediction database
inferredcites →https://doi.org/10.1093/nar/gks1068openalex-snapshot
Update on activities at the Universal Protein Resource (UniProt) in 2013
inferredcites →https://doi.org/10.1093/nar/gks539openalex-snapshot
SIFT web server: predicting effects of amino acid substitutions on proteins
inferredcites →https://doi.org/10.1093/nar/gkt1140openalex-snapshot
Activities at the Universal Protein Resource (UniProt)
inferredcites →https://doi.org/10.1093/protein/15.8.643openalex-snapshot
Sequence clustering strategies improve remote homology recognitions while reducing search times
inferredcites →https://doi.org/10.1186/1471-2105-11-383openalex-snapshot
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand
inferredcites →https://doi.org/10.1186/1471-2105-12-s4-s3openalex-snapshot
Improving the prediction of disease-related variants using protein three-dimensional structure
inferredcites →https://doi.org/10.1186/1471-2105-13-s4-s1openalex-snapshot
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
inferredcites →https://doi.org/10.1186/1471-2148-10-123openalex-snapshot
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach
inferredcites →https://doi.org/10.1186/gb-2002-3-8-research0040openalex-snapshot
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties
inferredcites →https://doi.org/10.1371/journal.pcbi.1000431openalex-snapshot
The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species
inferredcites →https://doi.org/10.1371/journal.pone.0003515openalex-snapshot
A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data
inferredcites →https://doi.org/10.1371/journal.pone.0018910openalex-snapshot
Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation
inferredcites →https://doi.org/10.1371/journal.pone.0054422openalex-snapshot
Increasing Sequence Search Sensitivity with Transitive Alignments
inferredcites →https://doi.org/10.4056/sigs.2945050openalex-snapshot
VIROME: a standard operating procedure for analysis of viral metagenome sequences
inferredcites →https://doi.org/10.4056/sigs.561626openalex-snapshot
Quantifying Protein Function Specificity in the Gene Ontology

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De novo assembly and functional annotation of the nervous system transcriptome in the Caribbean spiny lobster Panulirus argus
inferred← citeshttps://doi.org/10.1007/s00439-024-02692-zopenalex-snapshot
QAFI: a novel method for quantitative estimation of missense variant impact using protein-specific predictors and ensemble learning
inferred← citeshttps://doi.org/10.1007/s00521-023-08802-8openalex-snapshot
Language model-accelerated deep symbolic optimization
inferred← citeshttps://doi.org/10.1007/s00726-024-03422-5openalex-snapshot
LLM4THP: a computing tool to identify tumor homing peptides by molecular and sequence representation of large language model based on two-layer ensemble model strategy
inferred← citeshttps://doi.org/10.1007/s10126-026-10665-8openalex-snapshot
De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics
inferred← citeshttps://doi.org/10.1007/s10142-025-01641-xopenalex-snapshot
iACP-DPNet: a dual-pooling causal dilated convolutional network for interpretable anticancer peptide identification
inferred← citeshttps://doi.org/10.1007/s10340-021-01448-2openalex-snapshot
Investigating mechanisms associated with emamectin benzoate resistance in the tomato borer Tuta absoluta
inferred← citeshttps://doi.org/10.1007/s10618-024-01074-3openalex-snapshot
Missing value replacement in strings and applications
inferred← citeshttps://doi.org/10.1007/s10709-023-00196-8openalex-snapshot
Approaches to increase the validity of gene family identification using manual homology search tools
inferred← citeshttps://doi.org/10.1007/s10722-025-02661-zopenalex-snapshot
First short-read genome assembly and simple sequence repeat (SSR) mining of Typhonium flagelliforme, an anti-cancer medicinal plant
inferred← citeshttps://doi.org/10.1007/s10930-021-10003-yopenalex-snapshot
Protein Structure Prediction: Conventional and Deep Learning Perspectives
inferred← citeshttps://doi.org/10.1007/s10930-021-10016-7openalex-snapshot
Improved 3-D Protein Structure Predictions using Deep ResNet Model
inferred← citeshttps://doi.org/10.1007/s10930-022-10067-4openalex-snapshot
Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN)
inferred← citeshttps://doi.org/10.1007/s10969-016-9210-4openalex-snapshot
Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix
inferred← citeshttps://doi.org/10.1007/s11030-025-11402-4openalex-snapshot
DeepMCL-DTI: predicting drug-target interactions using multi-channel deep learning with attention mechanism
inferred← citeshttps://doi.org/10.1007/s11120-023-01018-wopenalex-snapshot
Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function
inferred← citeshttps://doi.org/10.1007/s11274-023-03718-wopenalex-snapshot
Repurposing miconazole and tamoxifen for the treatment of Mycobacterium abscessus complex infections through in silico chemogenomics approach
inferred← citeshttps://doi.org/10.1007/s11390-021-0851-9openalex-snapshot
DeepHBSP: A Deep Learning Framework for Predicting Human Blood-Secretory Proteins Using Transfer Learning
inferred← citeshttps://doi.org/10.1007/s11390-022-2158-xopenalex-snapshot
Connecting the Dots in Self-Supervised Learning: A Brief Survey for Beginners
inferred← citeshttps://doi.org/10.1007/s11432-024-4466-3openalex-snapshot
Large language models transform biological research: from architecture to utilization
inferred← citeshttps://doi.org/10.1007/s11704-022-2163-9openalex-snapshot
FragDPI: a novel drug-protein interaction prediction model based on fragment understanding and unified coding
inferred← citeshttps://doi.org/10.1007/s11704-025-41426-wopenalex-snapshot
A survey of geometric graph neural networks: data structures, models and applications
inferred← citeshttps://doi.org/10.1007/s11816-024-00920-6openalex-snapshot
Screening of heat stress-tolerant weedy rice and SNP identification of heat-tolerance-related genes
inferred← citeshttps://doi.org/10.1007/s13205-023-03483-5openalex-snapshot
Characterization and genome-wide sequence analysis of an ectomycorrhizal fungus Pisolithus albus, a potential source for reclamation of degraded lands
inferred← citeshttps://doi.org/10.1007/s13592-017-0542-2openalex-snapshot
RNA-Seq reveals that mitochondrial genes and long non-coding RNAs may play important roles in the bivoltine generations of the non-social Neotropical bee Tetrapedia diversipes
inferred← citeshttps://doi.org/10.1007/s13744-018-0590-yopenalex-snapshot
Biochemical Properties of α-Amylase from Midgut of Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae) Larvae
inferred← citeshttps://doi.org/10.1007/s40747-025-02065-7openalex-snapshot
Multi-feature enhanced protein language models for accurate protein-RNA binding residue prediction
inferred← citeshttps://doi.org/10.1007/s41060-022-00371-8openalex-snapshot
Learning to discover medicines
inferred← citeshttps://doi.org/10.1007/s42770-024-01406-xopenalex-snapshot
Drug to genome to drug: a computational large-scale chemogenomics screening for novel drug candidates against sporotrichosis
inferred← citeshttps://doi.org/10.1016/0009-2614(90)85614-iopenalex-snapshot
Phase shifts induced by transient Bloch-Siegert effects in NMR
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20267-7openalex-snapshot
Secondary Structure Prediction
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20449-4openalex-snapshot
Comparative Proteomic Analysis
inferred← citeshttps://doi.org/10.1016/b978-0-12-820546-4.00004-0openalex-snapshot
Database exploration: Selection and analysis of target protein structures
inferred← citeshttps://doi.org/10.1016/b978-0-323-90958-7.00008-xopenalex-snapshot
Revolution in microbial bioprospecting via the development of omics-based technologies
inferred← citeshttps://doi.org/10.1016/b978-0-44-332908-1.00023-4openalex-snapshot
Deep learning in protein structure prediction
inferred← citeshttps://doi.org/10.1016/bs.mie.2021.09.003openalex-snapshot
An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2
inferred← citeshttps://doi.org/10.1016/j.ab.2024.115603openalex-snapshot
PreDBP-PLMs: Prediction of DNA-binding proteins based on pre-trained protein language models and convolutional neural networks
inferred← citeshttps://doi.org/10.1016/j.ab.2024.115637openalex-snapshot
Protein-peptide binding residue prediction based on protein language models and cross-attention mechanism
inferred← citeshttps://doi.org/10.1016/j.ab.2024.115701openalex-snapshot
Alg-MFDL: A multi-feature deep learning framework for allergenic proteins prediction
inferred← citeshttps://doi.org/10.1016/j.ab.2025.115881openalex-snapshot
AFP-MCDF: Multi and cross-dimensional feature fusion methods for antifreeze protein prediction
inferred← citeshttps://doi.org/10.1016/j.ab.2025.116005openalex-snapshot
AHAPC: Multi-source feature fusion and ensemble learning for multiclass extremophilic protein prediction
inferred← citeshttps://doi.org/10.1016/j.ab.2025.116029openalex-snapshot
Classification prediction of drug target binding affinity based on the MolrProtTrans model
inferred← citeshttps://doi.org/10.1016/j.ajcnut.2024.10.011openalex-snapshot
Association of the EAT-Lancet diet, serial measures of serum proteome and gut microbiome, and cardiometabolic health: a prospective study of Chinese middle-aged and elderly adults
inferred← citeshttps://doi.org/10.1016/j.ajcnut.2025.06.026openalex-snapshot
Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study
inferred← citeshttps://doi.org/10.1016/j.algal.2018.05.004openalex-snapshot
Transcriptome analysis reveals the genetic foundation for the dynamics of starch and lipid production in Ettlia oleoabundans
inferred← citeshttps://doi.org/10.1016/j.algal.2022.102794openalex-snapshot
Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress
inferred← citeshttps://doi.org/10.1016/j.alit.2025.08.004openalex-snapshot
Predictive and therapeutic applications of protein language models
inferred← citeshttps://doi.org/10.1016/j.aquaculture.2026.744342openalex-snapshot
Comparative phenotypic and transcriptomic responses of full-siblings diploid and triploid Pacific oysters under extreme salinity stress
inferred← citeshttps://doi.org/10.1016/j.artmed.2025.103297openalex-snapshot
LkaM-PTM: Predicting PTM sites through multimodal protein features from capturing cross-field information
inferred← citeshttps://doi.org/10.1016/j.bbadis.2026.168184openalex-snapshot
Novel VARS1 variants define new clinical and molecular subtypes of a rare neurodevelopmental syndrome
inferred← citeshttps://doi.org/10.1016/j.bbagen.2024.130721openalex-snapshot
VotePLMs-AFP: Identification of antifreeze proteins using transformer-embedding features and ensemble learning
inferred← citeshttps://doi.org/10.1016/j.bbamem.2020.183272openalex-snapshot
Yeast recombinant production of intact human membrane proteins with long intrinsically disordered intracellular regions for structural studies
inferred← citeshttps://doi.org/10.1016/j.bbapap.2017.11.006openalex-snapshot
Structural insights of Rm Xyn10A – A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region
inferred← citeshttps://doi.org/10.1016/j.bbapap.2025.141100openalex-snapshot
Structure prediction and engineering of de novo proteins
inferred← citeshttps://doi.org/10.1016/j.bbih.2024.100814openalex-snapshot
Absence of association between maternal adverse events and long-term gut microbiome outcomes in the Australian autism biobank
inferred← citeshttps://doi.org/10.1016/j.biochi.2015.10.003openalex-snapshot
Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation
inferred← citeshttps://doi.org/10.1016/j.biologicals.2019.03.008openalex-snapshot
Use of a new RNA next generation sequencing approach for the specific detection of virus infection in cells
inferred← citeshttps://doi.org/10.1016/j.biombioe.2020.105573openalex-snapshot
Metagenomic analysis of autochthonous microbial biomass from banana waste: Screening design of factors that affect hydrogen production
inferred← citeshttps://doi.org/10.1016/j.biortech.2018.03.050openalex-snapshot
Metagenomic insight into methanogenic reactors promoting direct interspecies electron transfer via granular activated carbon
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2024.108399openalex-snapshot
Advancing microbial production through artificial intelligence-aided biology
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2026.108819openalex-snapshot
Computational methods for signal peptide prediction: From statistical models to deep learning
inferred← citeshttps://doi.org/10.1016/j.biteb.2023.101628openalex-snapshot
Uncovering the potential of landfill leachate for biodegradation of cassava-derived plastics
inferred← citeshttps://doi.org/10.1016/j.bmc.2017.05.050openalex-snapshot
A statistical view of protein chemical synthesis using NCL and extended methodologies
inferred← citeshttps://doi.org/10.1016/j.carres.2025.109453openalex-snapshot
ProtCB-bind: Protein-carbohydrate binding site prediction using an ensemble of classifiers
inferred← citeshttps://doi.org/10.1016/j.cbd.2025.101645openalex-snapshot
Investigating the molecular basis of cleptobiosis in eusocial stingless bees (Apidae: Hymenoptera)
inferred← citeshttps://doi.org/10.1016/j.cbpa.2021.04.004openalex-snapshot
Protein sequence design with deep generative models
inferred← citeshttps://doi.org/10.1016/j.cell.2018.05.008openalex-snapshot
Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota
inferred← citeshttps://doi.org/10.1016/j.cell.2018.10.029openalex-snapshot
US Immigration Westernizes the Human Gut Microbiome
inferred← citeshttps://doi.org/10.1016/j.cell.2019.03.040openalex-snapshot
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
inferred← citeshttps://doi.org/10.1016/j.cell.2019.10.014openalex-snapshot
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
inferred← citeshttps://doi.org/10.1016/j.cell.2020.04.019openalex-snapshot
The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants
inferred← citeshttps://doi.org/10.1016/j.cell.2021.05.002openalex-snapshot
A global metagenomic map of urban microbiomes and antimicrobial resistance
inferred← citeshttps://doi.org/10.1016/j.cell.2022.01.002openalex-snapshot
Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite
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