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SpliceSiteFinder-like (Riepe et al. 2021)

Configuration of SpliceSiteFinder-like: Alamut Visual 2.13; Classification cutoff per data set.

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Evaluations and results

3 evaluations · 33 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (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	Count (variants without a score)	False negatives	False positives	MCC	Negative predictive value	Precision	Recall	Specificity	True negatives	True positives
SpliceSiteFinder-like (Riepe et al. 2021)Evaluation	MYBPC3 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 5), MYBPC3 noncanonical splice-site variants (Riepe et al. benchmark set)	75% (best in column)	0 (best in column)	9 (best in column)	6	0.51 (best in column)	70%	81%	74% (best in column)	78% (best in column)	21	25
SpliceSiteFinder-like (Riepe et al. 2021)Evaluation	ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3), ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	63%	0 (best in column)	24	2 (best in column)	0.21	17%	95% (best in column)	63%	71%	5	40 (best in column)
SpliceSiteFinder-like (Riepe et al. 2021)Evaluation	ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4), ABCA4 deep-intronic variants (Riepe et al. benchmark set)	54%	0 (best in column)	10	27	0.06	77% (best in column)	29%	52%	55%	33 (best in column)	11

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	54% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'Accuracy (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	10 False negatives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'FN'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	27 False positives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'FP'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	0.06 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'MCC'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	0 Count (variants without a score) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'Missing values'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	77% Negative predictive value percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'NPV (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	29% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'PPV (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	52% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'Sensitivity (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	55% Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'Specificity (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	33 True negatives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'TN'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 deep-intronic variants: classification against mini- or midigene splicing results (Riepe et al. Table 4) Dataset: ABCA4 deep-intronic variants (Riepe et al. benchmark set)	11 True positives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 deep-intronic variants splicing-follow-up-20261009-protocol-riepe2021-abca4-di Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 4 row 'SpliceSiteFinder‐like', column 'TP'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	63% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'Accuracy (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	24 False negatives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'FN'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	2 False positives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'FP'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	0.21 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'MCC'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	0 Count (variants without a score) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'Missing values'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	17% Negative predictive value percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'NPV (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	95% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'PPV (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	63% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'Sensitivity (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	71% Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'Specificity (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	5 True negatives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'TN'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	40 True positives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'SpliceSiteFinder‐like', column 'TP'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: MYBPC3 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 5) Dataset: MYBPC3 noncanonical splice-site variants (Riepe et al. benchmark set)	75% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on MYBPC3 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-mybpc3-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 5 row 'SpliceSiteFinder‐like', column 'Accuracy (%)'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: MYBPC3 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 5) Dataset: MYBPC3 noncanonical splice-site variants (Riepe et al. benchmark set)	9 False negatives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on MYBPC3 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-mybpc3-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 5 row 'SpliceSiteFinder‐like', column 'FN'
Configuration: SpliceSiteFinder-like (Riepe et al. 2021)	Protocol: MYBPC3 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 5) Dataset: MYBPC3 noncanonical splice-site variants (Riepe et al. benchmark set)	6 False positives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceSiteFinder-like on MYBPC3 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-mybpc3-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 5 row 'SpliceSiteFinder‐like', column 'FP'

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Benchmarking deep learning splice prediction tools using functional splice assays · Original source · Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML

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Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-config-riepe2021-splicesitefinder-like

areas: dna-genomes
contexts: research
method types: conventional_pipeline
reported name: SpliceSiteFinder-like (Riepe et al. 2021)
foundation model eligible: false
version: Alamut Visual 2.13
parameters: Classification cutoff per data set; Table 2 prints the ROC-optimal thresholds, and Tables 3-5 do not restate which cutoff was applied
source locator: Methods 'In silico splice prediction tools'; Table 2
provenance note: SpliceSiteFinder-like (Riepe et al. 2021) as run in the cited comparison.

Related records

configuration of: SpliceSiteFinder-like
system: SpliceSiteFinder-like on ABCA4 deep-intronic variants
system: SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants
system: SpliceSiteFinder-like on MYBPC3 noncanonical splice-site variants

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