Protocol

Alternative polyadenylation coverage ratios (AlphaGenome paper)

Can predicted RNA coverage recover relative distal-versus-proximal polyadenylation-site usage?

Sources (3)

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21

0 evaluations · 0 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Dataset and biological context	PolyADB-annotated sites near gene boundaries; observed coverage ratios from tissue-pooled GTEx RNA-seq. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Split	Held-out test sites; the task paragraph does not identify the exact fold/site manifest. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Allowed inputs and adaptation	RNA-seq predictions and PolyADB site annotations; compare Borzoi coverage-ratio predictions. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Metrics as reported	spearmanr Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Aggregation	Spearman correlation of predicted versus observed coverage ratios. Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Uncertainty	Not reported for these summary-table scores. · Not reported in inspected sources Sources (3) AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

How it worksAlternative polyadenylation coverage ratios: evaluation procedure

Conceptual summary of the cited procedure; model-specific conditions are given below.

Sources (3)

What is tested

Can predicted RNA coverage recover relative distal-versus-proximal polyadenylation-site usage?

Sources (3)

Procedure

Derive polyadenylation-centric coverage ratios and compare with observed ratios for the distal/proximal sites.

Sources (3)

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

Papers and result coverage

Last literature check: 2026-09-17. Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.

Paper or primary resource	Version	Reference
alphagenome: Journal full-text XML	Retrieved page snapshot; no immutable publisher revision supplied	Read source
AlphaGenome Nature 2026 supplementary comparison tables	Nature version of record, 28 January 2026	Read source DOI: 10.1038/s41586-025-10014-0
AlphaGenome Nature 2026 supplementary methods	Supplement to Nature version of record, 28 January 2026; content hash pinned	Read source

What is still missing

Reported scores remain quarantined because the supplementary table and another source disagree; see the protocol limitations for the exact discrepancy.
Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.
Subsequent studies use different datasets and are not pooled with this paper.

Search and extraction details

source conflict quarantined

Searches

AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction
AlphaGenome independent evaluation benchmark 2026 variant effects

Evidence locations

'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

QUARANTINED NUMERICAL COMPARISON: Table3 row21 and article Sec9/Extended Data Fig6a report different model/comparator values. Preserve both origins; do not resolve the discrepancy or rank models from this row.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21
Primary artifact values differ and their evaluation equivalence is unresolved. The affected comparison is withheld from published result tables.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21

Profile review details

Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.

Stable record: alphagenome-2026-t3-protocol-12

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

45 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram steps ["Held-out annotated polyadenylation sites","Derive predicted coverage ratios","Compare with pooled observed ratios","Quarantine conflicting scalar reports"] Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Held-out annotated polyadenylation sites","Derive predicted coverage ratios","Compare with pooled observed ratios","Quarantine conflicting scalar reports"] Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram steps ["Held-out annotated polyadenylation sites","Derive predicted coverage ratios","Compare with pooled observed ratios","Quarantine conflicting scalar reports"] Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram title Alternative polyadenylation coverage ratios: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Alternative polyadenylation coverage ratios: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram title Alternative polyadenylation coverage ratios: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Dataset and biological context PolyADB-annotated sites near gene boundaries; observed coverage ratios from tissue-pooled GTEx RNA-seq. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release history

AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-t3-protocol-12

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 12
source table: 3
reference levels: metric: spearmanr; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H21; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
benchmark research: review date: 2026-09-17; status: source_conflict_quarantined; primary sources: evidence-official-56e5abfb5f12f1cd3b20; source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; inspected locators: 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21; searched queries: AlphaGenome benchmark evaluation Nature 2026 supplementary Tables 3 4 regulatory variant prediction; AlphaGenome independent evaluation benchmark 2026 variant effects; gaps: Reported scores remain quarantined because the supplementary table and another source disagree; see the protocol limitations for the exact discrepancy.; Individual protocol input manifests, scoring counts and uncertainty remain unextracted where explicitly marked.; Subsequent studies use different datasets and are not pooled with this paper.; claim scope: Original Nature paper comparison; numerical source transcription was separately reviewed. No independent model execution.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: p.22, Alternative Polyadenylation; paper: Sec9; Extended Data Fig.6a; tables: Suppl Table 3 Track performance; evaluation index 12; sheet rows 21; ambiguities: None recorded

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