Search and clustering orders of magnitude faster than BLAST
Datos Bibliográficos
| ID | 23323645 |
|---|---|
| Autores | R C Edgar (0000-0001-7355-2541, Tiburon Associates (United States), autor de correspondencia) |
| Año | 2010 |
| Volumen | 26 |
| Número | 19 |
| Páginas | 2460-2461 |
| Fecha de publicación | 2010-10-01 |
| Peer Reviewed | Sí |
| Open Access | Sí |
| Tipo | ARTICLE |
| Revista | Bioinformatics (JOURNAL) |
| Identificadores de la revista | ISSN: 1367-4803 • E-ISSN: 1367-4811 |
| Editorial | Oxford University Press (OUP) (PUBLISHER) |
| DOI | 10.1093/bioinformatics/btq461 |
| PMID | 20709691 |
| OpenAlex | W2124351063 |
| Idioma | EN |
| Citas recibidas | 88 |
| Referencias citadas | 8 |
Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.
Biology · Cluster analysis · Data mining · Exploit · Machine learning · Pattern recognition (psychology) · Sensitivity (control systems) · Sequence (biology) · Artificial Intelligence · Bioinformatics and Genomic Networks · Computer Science · Genomics and Phylogenetic Studies · Machine Learning in Bioinformatics
Gut Microbiota Diversity and Composition Across Shift Types and the Effects of Walnut Supplementation—An Observational and Interventional Study
Uparse
Screening wild and semi‐free ranging great apes for putative sexually transmitted diseases
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Uchime improves sensitivity and speed of chimera detection
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
The Silva ribosomal RNA gene database project
Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea
Contamination of the Arctic reflected in microbial metagenomes from the Greenland ice sheet
Fire severity influences the response of soil microbes to a boreal forest fire
The Effects of Pavement Types on Soil Bacterial Communities across Different Depths
Microbiological Contamination at Workplaces in a Combined Heat and Power (CHP) Station Processing Plant Biomass
Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area
Effect of Bioaugmentation on Biogas Yields and Kinetics in Anaerobic Digestion of Sewage Sludge
Anaerobic Dechlorination by a Humin-Dependent Pentachlorophenol-Dechlorinating Consortium under Autotrophic Conditions Induced by Homoacetogenesis
High microbiome diversity constricts the prevalence of human and animal pathogens in the plant rhizosphere worldwide
Dust at Various Workplaces—Microbiological and Toxicological Threats
Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area
Differences of Gut Microbiota in the Freshwater Blackworm (Lumbriculus variegatus
Anti-Biofouling Performance of an Immobilized Indigenous Quorum Quenching Bacterium Bacillus cereus HG10 and Its Influence on the Microbial Community in a Bioreactor
Revealing Cryptic Changes of Cyanobacterial Community Structure in Two Eutrophic Lakes Using eDNA Sequencing
Diversity and Distribution Characteristics of Soil Microbes across Forest–Peatland Ecotones in the Permafrost Regions
Comparative Study on Different Remediation Strategies Applied in Petroleum-Contaminated Soils
Pro-Inflammatory Oral Microbiota in Juvenile Spondyloarthritis
Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences
Effect of Humin and Chemical Factors on CO2-Fixing Acetogenesis and Methanogenesis
Rhizosphere Bacterial Community Structure and Predicted Functional Analysis in the Water-Level Fluctuation Zone of the Danjiangkou Reservoir in China During the Dry Period
Effects of Carbonaceous Materials with Different Structures on Cadmium Fractions and Microecology in Cadmium-Contaminated Soils
Impact of HLA-B27 and Disease Status on the Gut Microbiome of the Offspring of Ankylosing Spondylitis Patients
Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis
First Gut Content Analysis of 4th Instar Midge Larvae (Diptera
Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China
Response of soil characteristics and bacterial communities to nitrogen fertilization gradients in a coastal salt‐affected agroecosystem
Composition, activity and diversity of bacterial and fungal communities responses to inputs of phosphorus fertilizer enriched with beneficial microbes in degraded Brunic Arenosol
Biochar application induces different responses of bacterial and fungal communities to metabolic limitation
Simultaneously Improving Soil AMF Community and Phosphorus Uptake by Cotton Plants by Continuous Straw Incorporation and Optimizing Phosphorus Management
Effect of Elymus nutan s on the assemblage of arbuscular mycorrhizal fungal communities enhanced by soil available nitrogen in the restoration succession of revegetated grassland on the Qinghai‐Tibetan Plateau
Introducing sedum affects root‐soil interface phytoremediation of heavy metals in lei bamboo forest and potential risks from edible bamboo shoots
Dynamic variability of soil diazotrophs in bulk‐rhizosphere and phenological stages under long‐term mulching in an eroded area in the Loess Plateau
Degradation of soil arbuscular mycorrhizal fungal diversity and functionality accompanied by the aggravation of pepper Phytophthora blight in a facility shed in Southwest China
Composition and diversity of prokaryotes at an iron ore post‐mining site revealed the natural resilience 10 years after mining exploitation
Significant dose effects of fertilizers on soil diazotrophic diversity, community composition, and assembly processes in a long‐term paddy field fertilization experiment
Plantation type and afforestation age disclose variable influences on soil microbial compositions in man‐made forests in the Xiong'an New Area, China
Root architecture, root biomass and nutrient cycling in a mixed‐species agroforestry system
Soil bacterial community structure and co‐occurrence networks in response to the succession of secondary forests in subtropical regions
Enrichment of keystone fungal taxa after flue gas desulphurization gypsum application drives reclamation of the saline‐sodic soil
Soil organic matter and geochemical characteristics shape microbial community composition and structure across different land uses in an Australian wet tropical catchment
Community assembly processes of soil bacteria and fungi along a chronosequence of rice paddies cultivated on saline‐sodic land
Comparative effects of two humic substances on microbial dysbiosis in the rhizosphere soil where cucumber ( Cucumis sativus L.) is grown
Changes in the biological “regulators” of organic carbon mineralization in silted soils of check dams as a result of wet‐dry cycles
Urbanisation and habitat shape resource-driven dietary shifts in wild birds
The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya
Alaskan palaeosols in modern times
Novel mitochondrial haplotype of spotted-tailed quoll ( Dasyurus maculatus ) present on Kangaroo Island (South Australia) prior to extirpation
Identification of bacterial communities on different surface materials of museum artefacts using high throughput sequencing
Metabarcoding of root-associated ectomycorrhizal fungi of Himalayan pindrow fir through morphotyping and Next Generation Sequencing
Bacteria and fungi associated with isoprene consumption in soil
Responses of invasive grass’ microbial communities to water and nutrient stress treatments
Fungal community and functional responses to soil warming are greater than for soil nitrogen enrichment
Loss of deep roots limits biogenic agents of soil development that are only partially restored by decades of forest regeneration
Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms
Microbial community response to a decade of simulated global changes depends on the plant community
Microbial community response to drought depends on crop
Bacterial diversity and lipid biomarkers in sea ice and sinking particulate organic material during the melt season in the Canadian Arctic
A microbial perspective on the local influence of Arctic rivers and estuaries on Hudson Bay (Canada)
Releasing the microbes from old bones
Pathways linking caesarean delivery to early health in a dual burden context
Exploratory analysis reveals arthropod consumption in 10 lemur species using DNA metabarcoding
Screening wild and semi‐free ranging great apes for putative sexually transmitted diseases
Age‐related changes in the marmoset gut microbiome
Feasibility of fecal microbiota transplantation via oral gavage to safely alter gut microbiome composition in marmosets
Associations Between Gut Microbes and Social Behavior in Healthy 2-Year-Old Children
A Microbial Signature of Psychological Distress in Irritable Bowel Syndrome
Assessment of the phycosphere microbial dynamics of microbial community associated with red algae culture under different cultural conditions
Kansuiphorin C and Kansuinin A ameliorate malignant ascites by modulating gut microbiota and related metabolic functions
Fecal metabonomics combined with 16S rRNA gene sequencing to analyze the changes of gut microbiota in rats with kidney-yang deficiency syndrome and the intervention effect of You-gui pill
Health risk of Licorice-Yuanhua combination through induction of colonic H2S metabolism
Gancao-Gansui combination impacts gut microbiota diversity and related metabolic functions
Identification and action mechanism of lipid regulating components from Rhei Radix et rhizoma
Molokhia leaf extract prevents gut inflammation and obesity
Local geology determines responses of stream producers and fungal decomposers to nutrient enrichment
The efficacy of whole human genome capture on ancient dental calculus and dentin
High‐throughput sequencing of fecal DNA to identify insects consumed by wild W eddell's saddleback tamarins ( S aguinus weddelli , C ebidae, P rimates) in B olivia
Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma
Influence of fruit and invertebrate consumption on the gut microbiota of wild white‐faced capuchins ( Cebus capucinus )
Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white‐faced capuchins ( Cebus capucinus )
Bones, barcodes, and biodiversity
Environmental DNA reveals anthropogenic impacts on fish diversity in mountain streams and the increasing risk of species invasion
| Obras citantes distintas | 88 |
|---|---|
| Citas por año | 5,87 |
| Intervalo de citas | 2011 - 2026 (16) |
| Velocidad de citación | current |
| Altamente citado | No |
| Tipos de cita | Neutras: 85 |