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Paper · 25402007

Fast and sensitive protein alignment using DIAMOND.

Buchfink B and 2 others. Nat Methods, 2015. Cited by 9,684 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. Fast and sensitive protein alignment using DIAMOND. Papers, record 25402007. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/25402007

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title
Fast and sensitive protein alignment using DIAMOND.
PubMed
Journal
Nat Methods
PubMed
Year
2015
PubMed
Publication types
Comparative Study, Journal Article, Research Support, Non-U.S. Gov't
PubMed
Citations, by iCite
9,684
iCite
Relative citation ratio, by iCite
400
iCite
Revised in PubMed
2024-01-09
PubMed

Authors3

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

OrderAuthorForenameKindORCID iD
1Buchfink BBenjamin
2Xie CChao
3Huson DHDaniel H

Source PubMed

Topics9

NLM's MeSH indexing of the paper, its major topics first.

MeSH termMajor
MetagenomicsMajor topic
Sequence AlignmentMajor topic
SoftwareMajor topic
Algorithms
Base Sequence
Humans
Microbiota
Sensitivity and Specificity
Sequence Analysis, DNA

Source PubMed

Grants0

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

None in this release.

Trials1

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

TrialTitleThe trial lists it asNamed in the paper's record
NCT07169123Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBDBackground

Source ClinicalTrials.gov

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References21

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

OrderPMIDTitleJournalYearIn PapersSource
110,592,173KEGG: kyoto encyclopedia of genes and genomes.Nucleic Acids Res2000https://conductscience.org/library/papers/10592173PubMed
211,932,250BLAT--the BLAST-like alignment tool.Genome Res2002https://conductscience.org/library/papers/11932250PubMed
321,631,914Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.BMC Bioinformatics2011https://conductscience.org/library/papers/21631914PubMed
410,775,656Simplified amino acid alphabets for protein fold recognition and implications for folding.Protein Eng2000https://conductscience.org/library/papers/10775656PubMed
523,658,416A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.Bioinformatics2014https://conductscience.org/library/papers/23658416PubMed
617,943,116The human microbiome project.Nature2007https://conductscience.org/library/papers/17943116PubMed
715,608,212GenBank.Nucleic Acids Res2005https://conductscience.org/library/papers/15608212PubMed
811,934,743PatternHunter: faster and more sensitive homology search.Bioinformatics2002https://conductscience.org/library/papers/11934743PubMed
922,056,985Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.Nature2011https://conductscience.org/library/papers/22056985PubMed
109,818,143Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.Chem Biol1998https://conductscience.org/library/papers/9818143PubMed

1 to 10 of 21

See all 21 references

Cited by7,405

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 9,684 citations.

PMIDTitleJournalYearIn PapersSource
42,989,368Multi-omics analysis reveals microbial and metabolic signatures associated with neutral detergent fiber digestibility in dairy cattle.J Anim Sci Biotechnol2026https://conductscience.org/library/papers/42989368PubMed
42,989,114Effects of common antibiotics on representative gut bacterial strains associated with inflammatory bowel disease.BMC Microbiol2026https://conductscience.org/library/papers/42989114PubMed
42,989,098A project-aware and contamination-aware re-evaluation of host-unmapped reads in public Silene latifolia sequencing data.BMC Genomics2026https://conductscience.org/library/papers/42989098PubMed
42,983,652Complete genome sequence of mulberry dwarf phytoplasma strain MDAK-01: comparative genomics and evolutionary analyses.BMC Microbiol2026https://conductscience.org/library/papers/42983652PubMed
42,982,885A chromosomal-level genome assembly of Promethis valgipes Marseul, 1876 (Coleoptera: Tenebrionidae).Sci Data2026https://conductscience.org/library/papers/42982885PubMed
42,981,365Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils.PLoS One2026https://conductscience.org/library/papers/42981365PubMed
42,981,279Environmental enrichment is associated with changes in the gut microbiome and resistome of captive pythons.PLoS One2026https://conductscience.org/library/papers/42981279PubMed
42,980,911Effect of continuous application of pig manure on soil antibiotic resistance genes.Int Microbiol2026https://conductscience.org/library/papers/42980911PubMed
42,978,490The Potential Role of Gut Microbiome Dysbiosis and Functional Reprogramming in Colorectal Liver Metastasis via the Gut-Liver Axis.Cancer Rep (Hoboken)2026https://conductscience.org/library/papers/42978490PubMed
42,974,382A compact generative language model learns the compositional grammar of phase-separating proteins.Chem Sci2026https://conductscience.org/library/papers/42974382PubMed

1 to 10 of 7,405

See all 7,405 cited by

Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed
2026-11-06
PubMed
iCite
2026-11-05
iCite
PMC's ID file
2026-11-05
PMC's ID file
NIH RePORTER's grant and paper links
2026-11-01
NIH RePORTER's grant and paper links
Trials
2026-11-12
Gene search
2026-11-11
Pipelines
2026-09-18

Sources 11

  • ChEMBL, through Open TargetsCC BY-SA 3.0
  • ClinicalTrials.govNo license stated
  • HGNCCC0
  • iCiteCC BY 4.0
  • NCBI GenePublic domain (US government)
  • NIH RePORTER's grant and paper linksPublic domain
  • Open TargetsCC0 1.0
  • PMC's ID filePublic domain (US government)
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0
Each source's terms
  • ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • ClinicalTrials.govnone stated
  • HGNCCC0: https://www.genenames.org/about/license/
  • iCiteCC BY 4.0
  • NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
  • Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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