Configuration

BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)

BLAST 2.12.0 blastn, top hit, a configuration of BLAST (BLASTn): Custom nucleotide database from the training FASTA; task blastn; max_target_seqs = 1; label of the top hit.

3 evaluations · 14 results

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

3 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (16-class long-sequence RVDB dataset) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Accuracy (16-class long-sequence RVDB dataset)	Accuracy (33-class RVDB dataset)	Accuracy (40-class RVDB dataset)	Balanced accuracy (16-class long-sequence RVDB dataset)	Macro F1 (16-class long-sequence RVDB dataset)	Macro F1 (33-class RVDB dataset)	Macro F1 (40-class RVDB dataset)	MCC (16-class long-sequence RVDB dataset)	Precision (16-class long-sequence RVDB dataset, macro-averaged over classes)	Precision (33-class RVDB dataset, macro-averaged over classes)	Precision (40-class RVDB dataset, macro-averaged over classes)	Recall (16-class long-sequence RVDB dataset, macro-averaged over classes)	Recall (33-class RVDB dataset, macro-averaged over classes)	Recall (40-class RVDB dataset, macro-averaged over classes)
BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Evaluation	RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10), RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.977	Not reported	Not reported	0.977	0.977	Not reported	Not reported	0.975	0.978	Not reported	Not reported	0.977	Not reported	Not reported
BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Evaluation	RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7), RVDB C-RVDB v31.0 primary dataset, 33 refined classes	Not reported	0.968	Not reported	Not reported	Not reported	0.938	Not reported	Not reported	Not reported	0.94	Not reported	Not reported	0.939	Not reported
BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Evaluation	RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7), RVDB C-RVDB v31.0 primary dataset, 40 sampled classes	Not reported	Not reported	0.912	Not reported	Not reported	Not reported	0.889	Not reported	Not reported	Not reported	0.892	Not reported	Not reported	0.89

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.977 Accuracy (16-class long-sequence RVDB dataset) fraction · higher Uncertainty: 95% CI 0.950 to 0.989. Wilson binomial interval quoted in Section 3.8; method stated in Section 2.9 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLAST (blastn) on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'BLAST (blastn)', column 'Accuracy'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.977 Balanced accuracy (16-class long-sequence RVDB dataset) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLAST (blastn) on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'BLAST (blastn)', column 'Bal. Acc.'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.977 Macro F1 (16-class long-sequence RVDB dataset) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLAST (blastn) on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'BLAST (blastn)', column 'F1'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.975 MCC (16-class long-sequence RVDB dataset) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLAST (blastn) on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'BLAST (blastn)', column 'MCC'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.978 Precision (16-class long-sequence RVDB dataset, macro-averaged over classes) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLAST (blastn) on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'BLAST (blastn)', column 'Precision'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.977 Recall (16-class long-sequence RVDB dataset, macro-averaged over classes) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BLAST (blastn) on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'BLAST (blastn)', column 'Recall'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 33 refined classes	0.968 Accuracy (33-class RVDB dataset) fraction · higher Uncertainty: 95% CI 0.962 to 0.972. Wilson binomial interval quoted in Section 3.6, paragraph 1; method stated in Section 2.9 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 33-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '33 classes / blastn', column 'Accuracy'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 33 refined classes	0.938 Macro F1 (33-class RVDB dataset) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 33-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '33 classes / blastn', column 'F1'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 33 refined classes	0.94 Precision (33-class RVDB dataset, macro-averaged over classes) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 33-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '33 classes / blastn', column 'Precision'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 33 refined classes	0.939 Recall (33-class RVDB dataset, macro-averaged over classes) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 33-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '33 classes / blastn', column 'Recall'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes	0.912 Accuracy (40-class RVDB dataset) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 40-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'Accuracy'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes	0.889 Macro F1 (40-class RVDB dataset) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 40-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'F1'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes	0.892 Precision (40-class RVDB dataset, macro-averaged over classes) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 40-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'Precision'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)	Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7) Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes	0.89 Recall (40-class RVDB dataset, macro-averaged over classes) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source blastn on the RVDB 40-class dataset (BLAST comparison) gfm2-20261011-buzkova2026-protocol-blast-compare Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'Recall'

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Analyzing Genomic Foundation Models for Viral Sequence Identification · Original source · bioRxiv v1, posted 2026-09-28

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Technical metadata and extraction receipts

Stable ID: gfm2-20261011-buzkova2026-config-blastn

areas: dna-genomes
contexts: research
method types: conventional_pipeline
reported name: blastn
foundation model eligible: false
source locator: Section 2.8; Tables 7, 8 and 10
parameters: Custom nucleotide database from the training FASTA; task blastn; max_target_seqs = 1; label of the top hit
version: BLAST 2.12.0
provenance note: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026), as evaluated in the cited comparison.

Related records

configuration of: BLAST (BLASTn)
system: BLAST (blastn) on the RVDB long-sequence dataset, 16 classes
system: blastn on the RVDB 33-class dataset (BLAST comparison)
system: blastn on the RVDB 40-class dataset (BLAST comparison)

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